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Error: user-error ("Org export aborted. Unable to resolve link: \"introduction\" See `org-export-with-broken-links'") signal(user-error ("Org export aborted. Unable to resolve link: \"introduction\"\nSee `org-export-with-broken-links'")) user-error("Org export aborted. 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #41)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #47))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #41))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #42)) (link (:standard-properties [1851 nil 1905 1924 1927 1 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #46))) #("and " 0 4 (:parent #42)) (link (:standard-properties [1931 nil 1970 1978 1980 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #48))) #(".\n" 0 2 (:parent #42))) (paragraph (:standard-properties [1983 1983 1983 2118 2119 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #43)) (link (:standard-properties [2069 nil 2094 2114 2116 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #47))) #(".\n" 0 2 (:parent #43))))) (headline (:standard-properties [2119 2119 2130 2368 2368 0 (:title) nil nil nil nil 2132 2366 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 9) t] :title (#("Install" 0 7 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2130 2130 2130 2368 2368 0 nil section nil nil nil 2130 2368 nil # nil nil #36]) (paragraph (:standard-properties [2130 2130 2130 2367 2368 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #42)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #42] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #42))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #37]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #43)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #47)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("settings.py" 0 11 (:parent #51)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #43))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #45))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #47))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #38]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("Install redis. 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nil nil #42]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #45]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #48]) #("Note: we moved to MariaDB" 0 25 (:parent #51))) #("\n" 0 1 (:parent #48))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #49))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("As root configure and run\n" 0 26 (:parent #50))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #45] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # 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Currently we have two databases for deployment,\n'db" 0 163 (:parent #49)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("webqtl" 0 6 (:parent #53))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("s" 0 1 (:parent #54))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #49)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("webqtl" 0 6 (:parent #56))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("plant" 0 5 (:parent #57))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #49))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Download one database from\n" 0 27 (:parent #50))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #46]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #51))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #46]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #52))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Check the md5sum.\n" 0 18 (:parent #53))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #54))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #56))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("and\n" 0 4 (:parent #58))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #60))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #62))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #63))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Note for the plant database you can rename it to db" 0 51 (:parent #64)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #64] :use-brackets-p nil) #("webqtl" 0 6 (:parent #68))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #64] :use-brackets-p nil) #("s" 0 1 (:parent #69))) #(", or\nchange the settings in etc/default" 0 39 (:parent #64)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # 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nil nil #43] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #47))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #41]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # 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nil nil #45]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #48)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #48))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #46]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #52)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PATH" 0 4 (:parent #56))) #("and R" 0 5 (:parent #52)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("LIBS" 0 4 (:parent #58))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("SITE" 0 4 (:parent #59))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #52))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("On one system:\n" 0 15 (:parent #54))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #49] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #49]) #("and perhaps a few more.\n" 0 24 (:parent #56))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #47)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("data" 0 4 (:parent #59))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #47)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("files" 0 5 (:parent #61))) #("/genotype'" 0 10 (:parent #47))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #47]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #50]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #53)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("data" 0 4 (:parent #57))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #53)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("settings.py" 0 11 (:parent #59))) #("(see above in\nthis document).\n" 0 30 (:parent #53))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("You can use the GENENETWORK" 0 27 (:parent #54)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("FILES" 0 5 (:parent #58))) #("switch to set the datadir, for example\n" 0 39 (:parent #54))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #48))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #48]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #51]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #54))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #49))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #49]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #52]) #("This error\n" 0 11 (:parent #55))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #57))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #58)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("LIBS" 0 4 (:parent #62))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("SITE" 0 4 (:parent #63))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #58))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #50))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #50]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #53]) #("The following error\n" 0 20 (:parent #56))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #58))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #60))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #62)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("URI" 0 3 (:parent #66))) #("to something like\n" 0 18 (:parent #62))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #53] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #44))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #44]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #50))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("#+begin" 0 7 (:parent #51)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("src" 0 3 (:parent #55))) #("\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 #51))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #52))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #47]) #(" yes\n env GUIX" 0 30 (:parent #53)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #57))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PATH" 0 4 (:parent #58))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #53))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("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 #54))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #47]) #(" 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 #55)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #59))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("PATH" 0 4 (:parent #60))) #("=../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 #55))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("/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 #56))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #47]) #(" which should have the same HASH values " 0 48 (:parent #57)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #57]) #("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 #61))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #57)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #57] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #57)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #57] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #57)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #67))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PATH" 0 4 (:parent #68))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #57)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #57] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #57)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #72))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PATH" 0 4 (:parent #73))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #57)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #75))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PATH" 0 4 (:parent #76))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #57)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #57] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #57))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #25))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #20)]) #15)] :type unordered) #10 (item (:standard-properties [156 156 159 181 181 0 (:tag) item nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) #15] :bullet "- 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You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #357))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #359))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #361))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #352))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #352]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #355]) #("Install redis. 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nil nil #356]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #359]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #362]) #("Note: we moved to MariaDB" 0 25 (:parent #365))) #("\n" 0 1 (:parent #362))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #363))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("As root configure and run\n" 0 26 (:parent #364))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #359] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("If you want to run as root you may have to set\n" 0 47 (:parent #366))) (fixed-width (:standard-properties [3523 3523 nil nil 3563 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [3563 3563 3563 3584 3585 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("You also need to set\n" 0 21 (:parent #368))) (fixed-width (:standard-properties [3585 3585 nil nil 3608 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [3608 3608 3608 3687 3688 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #370))) (paragraph (:standard-properties [3688 3688 3688 3756 3757 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #371))) (fixed-width (:standard-properties [3757 3757 nil nil 3872 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #373))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("When you get errors like:\n" 0 26 (:parent #375))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("you may need to set\n" 0 20 (:parent #377))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #353] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #357))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #357]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #360]) #("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 #363)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("webqtl" 0 6 (:parent #367))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("s" 0 1 (:parent #368))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #363)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("webqtl" 0 6 (:parent #370))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("plant" 0 5 (:parent #371))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #363))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Download one database from\n" 0 27 (:parent #364))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #360]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #365] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #365))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #360]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #366))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Check the md5sum.\n" 0 18 (:parent #367))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #368))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #370))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("and\n" 0 4 (:parent #372))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #374))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #376))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("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 #377))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Note for the plant database you can rename it to db" 0 51 (:parent #378)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("webqtl" 0 6 (:parent #382))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("s" 0 1 (:parent #383))) #(", or\nchange the settings in etc/default" 0 39 (:parent #378)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("settings.py" 0 11 (:parent #385))) #("to match your path.\n" 0 20 (:parent #378)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #354))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #354]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #357]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #360))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #357] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #361] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #361))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #355))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #355]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("See " 0 4 (:parent #361)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #361] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #361))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #356))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #356]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #359]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #362)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #362] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #362))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #357))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #360))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #360]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #363]) #("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 #366)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("PATH" 0 4 (:parent #370))) #("and R" 0 5 (:parent #366)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("LIBS" 0 4 (:parent #372))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("SITE" 0 4 (:parent #373))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #366))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #363] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #363]) #("On one system:\n" 0 15 (:parent #368))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #363] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #363]) #("and perhaps a few more.\n" 0 24 (:parent #370))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #361)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #361] :use-brackets-p nil) #("data" 0 4 (:parent #373))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #361)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #361] :use-brackets-p nil) #("files" 0 5 (:parent #375))) #("/genotype'" 0 10 (:parent #361))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #361]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #364]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #367)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("data" 0 4 (:parent #371))) #(". 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 #367)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("settings.py" 0 11 (:parent #373))) #("(see above in\nthis document).\n" 0 30 (:parent #367))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #364]) #("You can use the GENENETWORK" 0 27 (:parent #368)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #368] :use-brackets-p nil) #("FILES" 0 5 (:parent #372))) #("switch to set the datadir, for example\n" 0 39 (:parent #368))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #364] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #362))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #362]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #365]) #("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 #368))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #363))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #363]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #366]) #("This error\n" 0 11 (:parent #369))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #366] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #366]) #("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 #371))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #366]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #372)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("LIBS" 0 4 (:parent #376))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("SITE" 0 4 (:parent #377))) #(". 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 #372))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #364))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #364]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #367]) #("The following error\n" 0 20 (:parent #370))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("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 #372))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #374))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #376)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #376] :use-brackets-p nil) #("URI" 0 3 (:parent #380))) #("to something like\n" 0 18 (:parent #376))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #367] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #358))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #358]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #361]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #364))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("#+begin" 0 7 (:parent #365)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("src" 0 3 (:parent #369))) #("\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 #365))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #366))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #361]) #(" yes\n env GUIX" 0 30 (:parent #367)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #371))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("PATH" 0 4 (:parent #372))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #367))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("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 #368))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #361]) #(" 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 #369)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #369] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #373))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #369] :use-brackets-p nil) #("PATH" 0 4 (:parent #374))) #("=../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 #369))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("/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 #370))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #361]) #(" which should have the same HASH values " 0 48 (:parent #371)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #371]) #("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 #375))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #371)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #371)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #371)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #381))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #382))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #371)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #371)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #386))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #387))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #371)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #389))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #390))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #371)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #371)))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((link (:standard-properties [124 nil 141 153 155 0 nil nil nil nil nil nil nil nil # nil nil (paragraph (:standard-properties [124 124 124 156 156 0 nil nil nil nil nil nil nil nil # 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nil nil (headline (:standard-properties [43 43 121 1231 1231 0 (:title) nil nil nil nil 123 1229 1 # nil nil (org-data (:standard-properties [1 1 1 15256 15256 0 nil org-data nil nil nil 3 15256 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 43 43 0 nil first-section nil nil nil 1 43 nil # nil nil #30]) (keyword (:standard-properties [1 1 nil nil 43 1 nil top-comment nil nil nil nil nil nil # nil nil #33] :key "TITLE" :value "Installing GeneNetwork services"))) #25 (headline (:standard-properties [1231 1231 1247 2119 2119 0 (:title) nil nil nil nil 1249 2117 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1247 1247 1247 2119 2119 0 nil section nil nil nil 1247 2119 nil # nil nil #35]) (paragraph (:standard-properties [1247 1247 1247 1632 1633 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Large system deployments can get very " 0 38 (:parent #41)) (link (:standard-properties [1285 nil 1337 1344 1346 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil) #("complex" 0 7 (:parent #45))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #41)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #47))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #41))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #42)) (link (:standard-properties [1851 nil 1905 1924 1927 1 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #46))) #("and " 0 4 (:parent #42)) (link (:standard-properties [1931 nil 1970 1978 1980 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #48))) #(".\n" 0 2 (:parent #42))) (paragraph (:standard-properties [1983 1983 1983 2118 2119 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #43)) (link (:standard-properties [2069 nil 2094 2114 2116 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #47))) #(".\n" 0 2 (:parent #43))))) (headline (:standard-properties [2119 2119 2130 2368 2368 0 (:title) nil nil nil nil 2132 2366 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 9) t] :title (#("Install" 0 7 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2130 2130 2130 2368 2368 0 nil section nil nil nil 2130 2368 nil # nil nil #36]) (paragraph (:standard-properties [2130 2130 2130 2367 2368 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #42)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #42] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #42))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #37]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #43)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #47)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("settings.py" 0 11 (:parent #51)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #43))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #45))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #47))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #38]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("Install redis. Make sure you add the setting:\n" 0 46 (:parent #44))) (fixed-width (:standard-properties [2913 2913 nil nil 2931 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "appendonly yes")))) (headline (:standard-properties [2931 2931 2952 5782 5782 0 (:title) nil nil nil nil 2954 5780 1 # nil nil #30] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [2952 2952 2986 4250 4250 0 (:title) section nil nil nil 2988 4248 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #42))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2986 2986 2986 4250 4250 0 nil section nil nil nil 2986 4250 nil # nil nil #42]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #45]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #48]) #("Note: we moved to MariaDB" 0 25 (:parent #51))) #("\n" 0 1 (:parent #48))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #49))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("As root configure and run\n" 0 26 (:parent #50))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #45] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("If you want to run as root you may have to set\n" 0 47 (:parent #52))) (fixed-width (:standard-properties [3523 3523 nil nil 3563 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [3563 3563 3563 3584 3585 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("You also need to set\n" 0 21 (:parent #54))) (fixed-width (:standard-properties [3585 3585 nil nil 3608 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [3608 3608 3608 3687 3688 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #56))) (paragraph (:standard-properties [3688 3688 3688 3756 3757 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #57))) (fixed-width (:standard-properties [3757 3757 nil nil 3872 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #59))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("When you get errors like:\n" 0 26 (:parent #61))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("you may need to set\n" 0 20 (:parent #63))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #43))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #43]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("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 #49)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("webqtl" 0 6 (:parent #53))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("s" 0 1 (:parent #54))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #49)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("webqtl" 0 6 (:parent #56))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("plant" 0 5 (:parent #57))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #49))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Download one database from\n" 0 27 (:parent #50))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #46]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #51))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #46]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #52))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Check the md5sum.\n" 0 18 (:parent #53))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #54))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #56))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("and\n" 0 4 (:parent #58))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #60))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #62))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #63))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Note for the plant database you can rename it to db" 0 51 (:parent #64)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #64] :use-brackets-p nil) #("webqtl" 0 6 (:parent #68))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #64] :use-brackets-p nil) #("s" 0 1 (:parent #69))) #(", or\nchange the settings in etc/default" 0 39 (:parent #64)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #64] :use-brackets-p nil) #("settings.py" 0 11 (:parent #71))) #("to match your path.\n" 0 20 (:parent #64)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #40]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #46))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #43] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #47))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #41]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("See " 0 4 (:parent #47)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #47))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #42]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #48)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #48))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #46]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #52)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PATH" 0 4 (:parent #56))) #("and R" 0 5 (:parent #52)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("LIBS" 0 4 (:parent #58))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("SITE" 0 4 (:parent #59))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #52))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("On one system:\n" 0 15 (:parent #54))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #49] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #49]) #("and perhaps a few more.\n" 0 24 (:parent #56))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #47)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("data" 0 4 (:parent #59))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #47)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("files" 0 5 (:parent #61))) #("/genotype'" 0 10 (:parent #47))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #47]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #50]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #53)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("data" 0 4 (:parent #57))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #53)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("settings.py" 0 11 (:parent #59))) #("(see above in\nthis document).\n" 0 30 (:parent #53))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("You can use the GENENETWORK" 0 27 (:parent #54)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("FILES" 0 5 (:parent #58))) #("switch to set the datadir, for example\n" 0 39 (:parent #54))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #48))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #48]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #51]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #54))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #49))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #49]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #52]) #("This error\n" 0 11 (:parent #55))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #57))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #58)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("LIBS" 0 4 (:parent #62))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("SITE" 0 4 (:parent #63))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #58))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #50))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #50]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #53]) #("The following error\n" 0 20 (:parent #56))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #58))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #60))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #62)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("URI" 0 3 (:parent #66))) #("to something like\n" 0 18 (:parent #62))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #53] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #44))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #44]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #50))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("#+begin" 0 7 (:parent #51)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("src" 0 3 (:parent #55))) #("\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 #51))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #52))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #47]) #(" yes\n env GUIX" 0 30 (:parent #53)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #57))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PATH" 0 4 (:parent #58))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #53))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("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 #54))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #47]) #(" 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 #55)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #59))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("PATH" 0 4 (:parent #60))) #("=../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 #55))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("/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 #56))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #47]) #(" which should have the same HASH values " 0 48 (:parent #57)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #57]) #("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 #61))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #57)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #57] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #57)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #57] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #57)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #67))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PATH" 0 4 (:parent #68))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #57)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #57] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #57)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #72))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PATH" 0 4 (:parent #73))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #57)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #75))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PATH" 0 4 (:parent #76))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #57)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #57] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #57))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #25))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #20)]) #15)] :type unordered) #10 (item (:standard-properties [156 156 159 181 181 0 (:tag) item nil nil nil nil nil nil # 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nil nil #46]) #("If you want to run as root you may have to set\n" 0 47 (:parent #53))) (fixed-width (:standard-properties [3523 3523 nil nil 3563 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [3563 3563 3563 3584 3585 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("You also need to set\n" 0 21 (:parent #55))) (fixed-width (:standard-properties [3585 3585 nil nil 3608 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [3608 3608 3608 3687 3688 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #57))) (paragraph (:standard-properties [3688 3688 3688 3756 3757 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #58))) (fixed-width (:standard-properties [3757 3757 nil nil 3872 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #60))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("When you get errors like:\n" 0 26 (:parent #62))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("you may need to set\n" 0 20 (:parent #64))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #40] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #44))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #44]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #50)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("webqtl" 0 6 (:parent #54))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("s" 0 1 (:parent #55))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #50)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("webqtl" 0 6 (:parent #57))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("plant" 0 5 (:parent #58))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #50))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Download one database from\n" 0 27 (:parent #51))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #47]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #52))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #47]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #53))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Check the md5sum.\n" 0 18 (:parent #54))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #55))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #57))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("and\n" 0 4 (:parent #59))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #61))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #63))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #64))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Note for the plant database you can rename it to db" 0 51 (:parent #65)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #65] :use-brackets-p nil) #("webqtl" 0 6 (:parent #69))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #65] :use-brackets-p nil) #("s" 0 1 (:parent #70))) #(", or\nchange the settings in etc/default" 0 39 (:parent #65)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #65] :use-brackets-p nil) #("settings.py" 0 11 (:parent #72))) #("to match your path.\n" 0 20 (:parent #65)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #41]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #47))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #44] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #48))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #42]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("See " 0 4 (:parent #48)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #48))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #43]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #49)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #49))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #44))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #44] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #47))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #47]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #50]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #53)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PATH" 0 4 (:parent #57))) #("and R" 0 5 (:parent #53)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("LIBS" 0 4 (:parent #59))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("SITE" 0 4 (:parent #60))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #53))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("On one system:\n" 0 15 (:parent #55))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #50] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #50]) #("and perhaps a few more.\n" 0 24 (:parent #57))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #44] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #48)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("data" 0 4 (:parent #60))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #48)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("files" 0 5 (:parent #62))) #("/genotype'" 0 10 (:parent #48))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #48]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #51]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #54)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("data" 0 4 (:parent #58))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #54)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("settings.py" 0 11 (:parent #60))) #("(see above in\nthis document).\n" 0 30 (:parent #54))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("You can use the GENENETWORK" 0 27 (:parent #55)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("FILES" 0 5 (:parent #59))) #("switch to set the datadir, for example\n" 0 39 (:parent #55))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #44] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #49))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #49]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #52]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #55))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #44] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #50))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #50]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #53]) #("This error\n" 0 11 (:parent #56))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("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 #58))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #59)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("LIBS" 0 4 (:parent #63))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("SITE" 0 4 (:parent #64))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #59))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #44] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #51))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #51]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #54]) #("The following error\n" 0 20 (:parent #57))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #54] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #54]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #59))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #54] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #54]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #61))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #54] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #54]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #63)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #63] :use-brackets-p nil) #("URI" 0 3 (:parent #67))) #("to something like\n" 0 18 (:parent #63))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #54] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #45))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #45]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #51))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("#+begin" 0 7 (:parent #52)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("src" 0 3 (:parent #56))) #("\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 #52))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #53))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #48]) #(" yes\n env GUIX" 0 30 (:parent #54)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #58))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("PATH" 0 4 (:parent #59))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #54))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("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 #55))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #48]) #(" 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 #56)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #60))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("PATH" 0 4 (:parent #61))) #("=../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 #56))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("/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 #57))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #48]) #(" which should have the same HASH values " 0 48 (:parent #58)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #58]) #("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 #62))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #58)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #58] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #58)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #58] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #58)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #68))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("PATH" 0 4 (:parent #69))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #58)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #58] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #58)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #73))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("PATH" 0 4 (:parent #74))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #58)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #76))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("PATH" 0 4 (:parent #77))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #58)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #58] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #58))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #26))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #21)]) #16)] :type unordered) #11 (item (:standard-properties [156 156 159 181 181 0 (:tag) item nil nil nil nil nil nil # 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nil nil #45]) #("If you want to run as root you may have to set\n" 0 47 (:parent #52))) (fixed-width (:standard-properties [3523 3523 nil nil 3563 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [3563 3563 3563 3584 3585 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("You also need to set\n" 0 21 (:parent #54))) (fixed-width (:standard-properties [3585 3585 nil nil 3608 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [3608 3608 3608 3687 3688 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #56))) (paragraph (:standard-properties [3688 3688 3688 3756 3757 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #57))) (fixed-width (:standard-properties [3757 3757 nil nil 3872 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #59))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("When you get errors like:\n" 0 26 (:parent #61))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("you may need to set\n" 0 20 (:parent #63))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #43))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #43]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("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 #49)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("webqtl" 0 6 (:parent #53))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("s" 0 1 (:parent #54))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #49)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("webqtl" 0 6 (:parent #56))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("plant" 0 5 (:parent #57))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #49))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Download one database from\n" 0 27 (:parent #50))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #46]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #51))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #46]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #52))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Check the md5sum.\n" 0 18 (:parent #53))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #54))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #56))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("and\n" 0 4 (:parent #58))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #60))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #62))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #63))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Note for the plant database you can rename it to db" 0 51 (:parent #64)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #64] :use-brackets-p nil) #("webqtl" 0 6 (:parent #68))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #64] :use-brackets-p nil) #("s" 0 1 (:parent #69))) #(", or\nchange the settings in etc/default" 0 39 (:parent #64)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #64] :use-brackets-p nil) #("settings.py" 0 11 (:parent #71))) #("to match your path.\n" 0 20 (:parent #64)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #40]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #46))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #43] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #47))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #41]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("See " 0 4 (:parent #47)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #47))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #42]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #48)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #48))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #46]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #52)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PATH" 0 4 (:parent #56))) #("and R" 0 5 (:parent #52)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("LIBS" 0 4 (:parent #58))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("SITE" 0 4 (:parent #59))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #52))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("On one system:\n" 0 15 (:parent #54))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #49] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #49]) #("and perhaps a few more.\n" 0 24 (:parent #56))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #47)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("data" 0 4 (:parent #59))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #47)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("files" 0 5 (:parent #61))) #("/genotype'" 0 10 (:parent #47))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #47]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #50]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #53)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("data" 0 4 (:parent #57))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #53)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("settings.py" 0 11 (:parent #59))) #("(see above in\nthis document).\n" 0 30 (:parent #53))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("You can use the GENENETWORK" 0 27 (:parent #54)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("FILES" 0 5 (:parent #58))) #("switch to set the datadir, for example\n" 0 39 (:parent #54))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #48))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #48]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #51]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #54))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #49))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #49]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #52]) #("This error\n" 0 11 (:parent #55))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #57))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #58)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("LIBS" 0 4 (:parent #62))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("SITE" 0 4 (:parent #63))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #58))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #50))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #50]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #53]) #("The following error\n" 0 20 (:parent #56))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #58))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #60))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #62)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("URI" 0 3 (:parent #66))) #("to something like\n" 0 18 (:parent #62))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #53] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #44))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #44]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #50))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("#+begin" 0 7 (:parent #51)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("src" 0 3 (:parent #55))) #("\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 #51))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #52))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #47]) #(" yes\n env GUIX" 0 30 (:parent #53)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #57))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PATH" 0 4 (:parent #58))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #53))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("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 #54))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #47]) #(" 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 #55)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #59))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("PATH" 0 4 (:parent #60))) #("=../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 #55))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("/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 #56))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #47]) #(" which should have the same HASH values " 0 48 (:parent #57)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #57]) #("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 #61))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #57)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #57] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #57)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #57] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #57)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #67))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PATH" 0 4 (:parent #68))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #57)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #57] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #57)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #72))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PATH" 0 4 (:parent #73))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #57)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #75))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PATH" 0 4 (:parent #76))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #57)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #57] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #57))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #25))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #20)]) #15)] :type unordered) #10 (item (:standard-properties [156 156 159 181 181 0 (:tag) item nil nil nil nil nil nil # 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nil nil #40]) #("If you want to run as root you may have to set\n" 0 47 (:parent #47))) (fixed-width (:standard-properties [3523 3523 nil nil 3563 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [3563 3563 3563 3584 3585 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("You also need to set\n" 0 21 (:parent #49))) (fixed-width (:standard-properties [3585 3585 nil nil 3608 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [3608 3608 3608 3687 3688 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #51))) (paragraph (:standard-properties [3688 3688 3688 3756 3757 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #52))) (fixed-width (:standard-properties [3757 3757 nil nil 3872 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #54))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("When you get errors like:\n" 0 26 (:parent #56))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("you may need to set\n" 0 20 (:parent #58))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #38))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #38]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #44)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("webqtl" 0 6 (:parent #48))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("s" 0 1 (:parent #49))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #44)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("webqtl" 0 6 (:parent #51))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("plant" 0 5 (:parent #52))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #44))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Download one database from\n" 0 27 (:parent #45))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #41]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #46))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #41]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #47))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Check the md5sum.\n" 0 18 (:parent #48))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #49))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #51))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("and\n" 0 4 (:parent #53))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #55))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #57))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #58))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Note for the plant database you can rename it to db" 0 51 (:parent #59)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("webqtl" 0 6 (:parent #63))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("s" 0 1 (:parent #64))) #(", or\nchange the settings in etc/default" 0 39 (:parent #59)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("settings.py" 0 11 (:parent #66))) #("to match your path.\n" 0 20 (:parent #59)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #35]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #41))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #38] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #42))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #36]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("See " 0 4 (:parent #42)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #42))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #37]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #43)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #43))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #41))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #41]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #47)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PATH" 0 4 (:parent #51))) #("and R" 0 5 (:parent #47)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("LIBS" 0 4 (:parent #53))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("SITE" 0 4 (:parent #54))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #47))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("On one system:\n" 0 15 (:parent #49))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #44] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #44]) #("and perhaps a few more.\n" 0 24 (:parent #51))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #42)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("data" 0 4 (:parent #54))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #42)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("files" 0 5 (:parent #56))) #("/genotype'" 0 10 (:parent #42))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #42]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #48)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("data" 0 4 (:parent #52))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #48)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("settings.py" 0 11 (:parent #54))) #("(see above in\nthis document).\n" 0 30 (:parent #48))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("You can use the GENENETWORK" 0 27 (:parent #49)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("FILES" 0 5 (:parent #53))) #("switch to set the datadir, for example\n" 0 39 (:parent #49))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #43))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #43]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #46]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #49))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #44))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #44]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("This error\n" 0 11 (:parent #50))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("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 #52))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #53)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("LIBS" 0 4 (:parent #57))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("SITE" 0 4 (:parent #58))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #53))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #45]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("The following error\n" 0 20 (:parent #51))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #53))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #55))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #57)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("URI" 0 3 (:parent #61))) #("to something like\n" 0 18 (:parent #57))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #48] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #39]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #45))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("#+begin" 0 7 (:parent #46)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("src" 0 3 (:parent #50))) #("\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 #46))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #47))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #42]) #(" yes\n env GUIX" 0 30 (:parent #48)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #52))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PATH" 0 4 (:parent #53))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #48))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #49))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #42]) #(" 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 #50)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #54))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PATH" 0 4 (:parent #55))) #("=../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 #50))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("/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 #51))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #42]) #(" which should have the same HASH values " 0 48 (:parent #52)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #52]) #("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 #56))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #52)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #52)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #52)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #62))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PATH" 0 4 (:parent #63))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #52)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #52)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #67))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PATH" 0 4 (:parent #68))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #52)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #70))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PATH" 0 4 (:parent #71))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #52)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #52))))))] :pre-blank 0 :raw-value 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #355)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #355] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #361))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #355))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #352]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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Follow the instructions on\n" 0 117 (:parent #356)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #356] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. 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You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #357))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #359))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #361))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #352))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #352]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #355]) #("Install redis. 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Login as root\n" 0 46 (:parent #370))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("and\n" 0 4 (:parent #372))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #374))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #376))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("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 #377))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Note for the plant database you can rename it to db" 0 51 (:parent #378)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("webqtl" 0 6 (:parent #382))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("s" 0 1 (:parent #383))) #(", or\nchange the settings in etc/default" 0 39 (:parent #378)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("settings.py" 0 11 (:parent #385))) #("to match your path.\n" 0 20 (:parent #378)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #354))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #354]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #357]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #360))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #357] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #361] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #361))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #355))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #355]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("See " 0 4 (:parent #361)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #361] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #361))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #356))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #356]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #359]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #362)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #362] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #362))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #357))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #360))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #360]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #363]) #("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 #366)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("PATH" 0 4 (:parent #370))) #("and R" 0 5 (:parent #366)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("LIBS" 0 4 (:parent #372))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("SITE" 0 4 (:parent #373))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #366))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #363] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #363]) #("On one system:\n" 0 15 (:parent #368))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #363] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #363]) #("and perhaps a few more.\n" 0 24 (:parent #370))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #361)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #361] :use-brackets-p nil) #("data" 0 4 (:parent #373))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #361)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #361] :use-brackets-p nil) #("files" 0 5 (:parent #375))) #("/genotype'" 0 10 (:parent #361))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #361]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #364]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #367)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("data" 0 4 (:parent #371))) #(". 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 #367)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("settings.py" 0 11 (:parent #373))) #("(see above in\nthis document).\n" 0 30 (:parent #367))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #364]) #("You can use the GENENETWORK" 0 27 (:parent #368)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #368] :use-brackets-p nil) #("FILES" 0 5 (:parent #372))) #("switch to set the datadir, for example\n" 0 39 (:parent #368))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #364] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #362))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #362]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #365]) #("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 #368))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #363))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #363]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #366]) #("This error\n" 0 11 (:parent #369))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #366] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #366]) #("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 #371))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #366]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #372)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("LIBS" 0 4 (:parent #376))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("SITE" 0 4 (:parent #377))) #(". 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 #372))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #364))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #364]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #367]) #("The following error\n" 0 20 (:parent #370))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("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 #372))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #374))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #376)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #376] :use-brackets-p nil) #("URI" 0 3 (:parent #380))) #("to something like\n" 0 18 (:parent #376))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #367] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #358))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #358]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #361]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #364))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("#+begin" 0 7 (:parent #365)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("src" 0 3 (:parent #369))) #("\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 #365))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #366))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #361]) #(" yes\n env GUIX" 0 30 (:parent #367)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #371))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("PATH" 0 4 (:parent #372))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #367))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("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 #368))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #361]) #(" 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 #369)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #369] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #373))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #369] :use-brackets-p nil) #("PATH" 0 4 (:parent #374))) #("=../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 #369))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("/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 #370))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #361]) #(" which should have the same HASH values " 0 48 (:parent #371)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #371]) #("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 #375))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #371)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #371)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #371)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #381))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #382))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #371)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #371)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #386))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #387))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #371)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #389))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #390))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #371)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #371)))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((paragraph (:standard-properties [124 124 124 156 156 0 nil nil nil nil nil nil nil nil # 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nil nil (headline (:standard-properties [43 43 121 1231 1231 0 (:title) nil nil nil nil 123 1229 1 # nil nil (org-data (:standard-properties [1 1 1 15256 15256 0 nil org-data nil nil nil 3 15256 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 43 43 0 nil first-section nil nil nil 1 43 nil # nil nil #25]) (keyword (:standard-properties [1 1 nil nil 43 1 nil top-comment nil nil nil nil nil nil # nil nil #28] :key "TITLE" :value "Installing GeneNetwork services"))) #20 (headline (:standard-properties [1231 1231 1247 2119 2119 0 (:title) nil nil nil nil 1249 2117 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #30))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1247 1247 1247 2119 2119 0 nil section nil nil nil 1247 2119 nil # nil nil #30]) (paragraph (:standard-properties [1247 1247 1247 1632 1633 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("Large system deployments can get very " 0 38 (:parent #36)) (link (:standard-properties [1285 nil 1337 1344 1346 0 nil nil nil nil nil nil nil nil # nil nil #36] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil) #("complex" 0 7 (:parent #40))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #36)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #36] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #42))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #36))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #37)) (link (:standard-properties [1851 nil 1905 1924 1927 1 nil nil nil nil nil nil nil nil # nil nil #37] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #41))) #("and " 0 4 (:parent #37)) (link (:standard-properties [1931 nil 1970 1978 1980 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #43))) #(".\n" 0 2 (:parent #37))) (paragraph (:standard-properties [1983 1983 1983 2118 2119 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #38)) (link (:standard-properties [2069 nil 2094 2114 2116 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #42))) #(".\n" 0 2 (:parent #38))))) (headline (:standard-properties [2119 2119 2130 2368 2368 0 (:title) nil nil nil nil 2132 2366 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 9) t] :title (#("Install" 0 7 (:parent #31))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2130 2130 2130 2368 2368 0 nil section nil nil nil 2130 2368 nil # nil nil #31]) (paragraph (:standard-properties [2130 2130 2130 2367 2368 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #37)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #37] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #37))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #32]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #38)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #42)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("settings.py" 0 11 (:parent #46)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #38))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #40))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #42))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #33]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("Install redis. 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nil nil #37]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #40]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #43]) #("Note: we moved to MariaDB" 0 25 (:parent #46))) #("\n" 0 1 (:parent #43))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #44))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("As root configure and run\n" 0 26 (:parent #45))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #40] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("If you want to run as root you may have to set\n" 0 47 (:parent #47))) (fixed-width (:standard-properties [3523 3523 nil nil 3563 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [3563 3563 3563 3584 3585 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("You also need to set\n" 0 21 (:parent #49))) (fixed-width (:standard-properties [3585 3585 nil nil 3608 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [3608 3608 3608 3687 3688 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #51))) (paragraph (:standard-properties [3688 3688 3688 3756 3757 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #52))) (fixed-width (:standard-properties [3757 3757 nil nil 3872 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #54))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("When you get errors like:\n" 0 26 (:parent #56))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("you may need to set\n" 0 20 (:parent #58))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #38))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #38]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #44)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("webqtl" 0 6 (:parent #48))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("s" 0 1 (:parent #49))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #44)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("webqtl" 0 6 (:parent #51))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("plant" 0 5 (:parent #52))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #44))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Download one database from\n" 0 27 (:parent #45))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #41]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #46))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #41]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #47))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Check the md5sum.\n" 0 18 (:parent #48))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #49))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #51))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("and\n" 0 4 (:parent #53))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #55))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #57))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #58))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Note for the plant database you can rename it to db" 0 51 (:parent #59)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("webqtl" 0 6 (:parent #63))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("s" 0 1 (:parent #64))) #(", or\nchange the settings in etc/default" 0 39 (:parent #59)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("settings.py" 0 11 (:parent #66))) #("to match your path.\n" 0 20 (:parent #59)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #35]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #41))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #38] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #42))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #36]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("See " 0 4 (:parent #42)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #42))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #37]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #43)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #43))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #41))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #41]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #47)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PATH" 0 4 (:parent #51))) #("and R" 0 5 (:parent #47)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("LIBS" 0 4 (:parent #53))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("SITE" 0 4 (:parent #54))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #47))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("On one system:\n" 0 15 (:parent #49))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #44] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #44]) #("and perhaps a few more.\n" 0 24 (:parent #51))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #42)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("data" 0 4 (:parent #54))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #42)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("files" 0 5 (:parent #56))) #("/genotype'" 0 10 (:parent #42))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #42]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #48)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("data" 0 4 (:parent #52))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #48)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("settings.py" 0 11 (:parent #54))) #("(see above in\nthis document).\n" 0 30 (:parent #48))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("You can use the GENENETWORK" 0 27 (:parent #49)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("FILES" 0 5 (:parent #53))) #("switch to set the datadir, for example\n" 0 39 (:parent #49))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #43))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #43]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #46]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #49))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #44))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #44]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("This error\n" 0 11 (:parent #50))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("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 #52))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #53)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("LIBS" 0 4 (:parent #57))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("SITE" 0 4 (:parent #58))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #53))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #45]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("The following error\n" 0 20 (:parent #51))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #53))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #55))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #57)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("URI" 0 3 (:parent #61))) #("to something like\n" 0 18 (:parent #57))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #48] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #39]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #45))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("#+begin" 0 7 (:parent #46)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("src" 0 3 (:parent #50))) #("\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 #46))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #47))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #42]) #(" yes\n env GUIX" 0 30 (:parent #48)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #52))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PATH" 0 4 (:parent #53))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #48))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #49))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #42]) #(" 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 #50)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #54))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PATH" 0 4 (:parent #55))) #("=../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 #50))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("/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 #51))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #42]) #(" which should have the same HASH values " 0 48 (:parent #52)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #52]) #("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 #56))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #52)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #52)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #52)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #62))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PATH" 0 4 (:parent #63))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #52)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #52)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #67))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PATH" 0 4 (:parent #68))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #52)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #70))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PATH" 0 4 (:parent #71))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #52)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #52))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #20))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #15)]) #10)] :type unordered) #5 (item (:standard-properties [156 156 159 181 181 0 (:tag) item nil nil nil nil nil nil # 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #37)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #43))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #37))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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nil nil #39] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #43))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #37]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("See " 0 4 (:parent #43)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #43))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #38]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #44)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #44))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #42))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #42]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #48)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PATH" 0 4 (:parent #52))) #("and R" 0 5 (:parent #48)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("LIBS" 0 4 (:parent #54))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("SITE" 0 4 (:parent #55))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #48))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("On one system:\n" 0 15 (:parent #50))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #45] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #45]) #("and perhaps a few more.\n" 0 24 (:parent #52))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #43)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("data" 0 4 (:parent #55))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #43)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("files" 0 5 (:parent #57))) #("/genotype'" 0 10 (:parent #43))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #43]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #49)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("data" 0 4 (:parent #53))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #49)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("settings.py" 0 11 (:parent #55))) #("(see above in\nthis document).\n" 0 30 (:parent #49))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("You can use the GENENETWORK" 0 27 (:parent #50)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("FILES" 0 5 (:parent #54))) #("switch to set the datadir, for example\n" 0 39 (:parent #50))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #44))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #44]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #47]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #50))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #45]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("This error\n" 0 11 (:parent #51))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #53))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #54)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("LIBS" 0 4 (:parent #58))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("SITE" 0 4 (:parent #59))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #54))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #46]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("The following error\n" 0 20 (:parent #52))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #54))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #56))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #58)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("URI" 0 3 (:parent #62))) #("to something like\n" 0 18 (:parent #58))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #49] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #40]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #46))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("#+begin" 0 7 (:parent #47)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("src" 0 3 (:parent #51))) #("\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 #47))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #48))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #43]) #(" yes\n env GUIX" 0 30 (:parent #49)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #53))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PATH" 0 4 (:parent #54))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #49))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("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 #50))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #43]) #(" 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 #51)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #55))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PATH" 0 4 (:parent #56))) #("=../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 #51))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("/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 #52))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #43]) #(" which should have the same HASH values " 0 48 (:parent #53)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #53]) #("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 #57))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #53)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #53)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #53] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #53)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #63))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PATH" 0 4 (:parent #64))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #53)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #53)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #68))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PATH" 0 4 (:parent #69))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #53)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #31)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #31] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #37))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #31))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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nil nil #33] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #37))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #31))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #31]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("See " 0 4 (:parent #37)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #37))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #32]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #38)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #38))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #36))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #36]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #42)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("PATH" 0 4 (:parent #46))) #("and R" 0 5 (:parent #42)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("LIBS" 0 4 (:parent #48))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("SITE" 0 4 (:parent #49))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #42))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("On one system:\n" 0 15 (:parent #44))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #39] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #39]) #("and perhaps a few more.\n" 0 24 (:parent #46))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #37)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("data" 0 4 (:parent #49))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #37)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("files" 0 5 (:parent #51))) #("/genotype'" 0 10 (:parent #37))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #37]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #43)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("data" 0 4 (:parent #47))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #43)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("settings.py" 0 11 (:parent #49))) #("(see above in\nthis document).\n" 0 30 (:parent #43))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("You can use the GENENETWORK" 0 27 (:parent #44)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("FILES" 0 5 (:parent #48))) #("switch to set the datadir, for example\n" 0 39 (:parent #44))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #38))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #38]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #41]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #44))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #39))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #39]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("This error\n" 0 11 (:parent #45))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #47))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #48)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("LIBS" 0 4 (:parent #52))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("SITE" 0 4 (:parent #53))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #48))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #40))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #40]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("The following error\n" 0 20 (:parent #46))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #48))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #50))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #52)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("URI" 0 3 (:parent #56))) #("to something like\n" 0 18 (:parent #52))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #43] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #34]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #40))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("#+begin" 0 7 (:parent #41)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("src" 0 3 (:parent #45))) #("\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 #41))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #42))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #37]) #(" yes\n env GUIX" 0 30 (:parent #43)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #47))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("PATH" 0 4 (:parent #48))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #43))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("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 #44))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #37]) #(" 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 #45)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #49))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("PATH" 0 4 (:parent #50))) #("=../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 #45))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("/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 #46))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #37]) #(" which should have the same HASH values " 0 48 (:parent #47)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #47]) #("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 #51))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #47)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #47)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #47)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #57))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PATH" 0 4 (:parent #58))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #47)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #47)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #62))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PATH" 0 4 (:parent #63))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #47)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #65))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PATH" 0 4 (:parent #66))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #47)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #47))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #15))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #10)]) #5)] :type unordered) #0 (item (:standard-properties [156 156 159 181 181 0 (:tag) item nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) #5] :bullet "- " 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You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #357))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #359))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #361))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #352))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #352]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #355]) #("Install redis. Make sure you add the setting:\n" 0 46 (:parent #358))) (fixed-width (:standard-properties [2913 2913 nil nil 2931 2 nil nil nil nil nil nil nil nil # nil nil #355] :value "appendonly yes")))) (headline (:standard-properties [2931 2931 2952 5782 5782 0 (:title) nil nil nil nil 2954 5780 1 # nil nil #344] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #353))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [2952 2952 2986 4250 4250 0 (:title) section nil nil nil 2988 4248 2 # nil nil #353] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #356))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2986 2986 2986 4250 4250 0 nil section nil nil nil 2986 4250 nil # nil nil #356]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #359]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #362]) #("Note: we moved to MariaDB" 0 25 (:parent #365))) #("\n" 0 1 (:parent #362))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #363))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("As root configure and run\n" 0 26 (:parent #364))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #359] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("If you want to run as root you may have to set\n" 0 47 (:parent #366))) (fixed-width (:standard-properties [3523 3523 nil nil 3563 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [3563 3563 3563 3584 3585 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("You also need to set\n" 0 21 (:parent #368))) (fixed-width (:standard-properties [3585 3585 nil nil 3608 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [3608 3608 3608 3687 3688 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #370))) (paragraph (:standard-properties [3688 3688 3688 3756 3757 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #371))) (fixed-width (:standard-properties [3757 3757 nil nil 3872 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #373))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("When you get errors like:\n" 0 26 (:parent #375))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("you may need to set\n" 0 20 (:parent #377))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #353] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #357))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #357]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #360]) #("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 #363)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("webqtl" 0 6 (:parent #367))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("s" 0 1 (:parent #368))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #363)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("webqtl" 0 6 (:parent #370))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("plant" 0 5 (:parent #371))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #363))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Download one database from\n" 0 27 (:parent #364))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #360]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #365] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #365))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #360]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #366))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Check the md5sum.\n" 0 18 (:parent #367))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #368))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #370))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("and\n" 0 4 (:parent #372))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #374))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #376))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("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 #377))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Note for the plant database you can rename it to db" 0 51 (:parent #378)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("webqtl" 0 6 (:parent #382))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("s" 0 1 (:parent #383))) #(", or\nchange the settings in etc/default" 0 39 (:parent #378)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("settings.py" 0 11 (:parent #385))) #("to match your path.\n" 0 20 (:parent #378)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #354))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #354]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #357]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #360))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #357] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #361] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #361))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #355))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #355]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("See " 0 4 (:parent #361)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #361] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #361))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #356))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #356]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #359]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #362)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #362] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #362))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #357))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #360))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #360]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #363]) #("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 #366)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("PATH" 0 4 (:parent #370))) #("and R" 0 5 (:parent #366)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("LIBS" 0 4 (:parent #372))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("SITE" 0 4 (:parent #373))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #366))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #363] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #363]) #("On one system:\n" 0 15 (:parent #368))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #363] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #363]) #("and perhaps a few more.\n" 0 24 (:parent #370))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #361)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #361] :use-brackets-p nil) #("data" 0 4 (:parent #373))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #361)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #361] :use-brackets-p nil) #("files" 0 5 (:parent #375))) #("/genotype'" 0 10 (:parent #361))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #361]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #364]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #367)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("data" 0 4 (:parent #371))) #(". 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 #367)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("settings.py" 0 11 (:parent #373))) #("(see above in\nthis document).\n" 0 30 (:parent #367))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #364]) #("You can use the GENENETWORK" 0 27 (:parent #368)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #368] :use-brackets-p nil) #("FILES" 0 5 (:parent #372))) #("switch to set the datadir, for example\n" 0 39 (:parent #368))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #364] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #362))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #362]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #365]) #("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 #368))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #363))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #363]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #366]) #("This error\n" 0 11 (:parent #369))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #366] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #366]) #("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 #371))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #366]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #372)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("LIBS" 0 4 (:parent #376))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("SITE" 0 4 (:parent #377))) #(". 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 #372))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #364))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #364]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #367]) #("The following error\n" 0 20 (:parent #370))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("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 #372))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #374))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #376)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #376] :use-brackets-p nil) #("URI" 0 3 (:parent #380))) #("to something like\n" 0 18 (:parent #376))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #367] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #358))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #358]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #361]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #364))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("#+begin" 0 7 (:parent #365)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("src" 0 3 (:parent #369))) #("\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 #365))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #366))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #361]) #(" yes\n env GUIX" 0 30 (:parent #367)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #371))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("PATH" 0 4 (:parent #372))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #367))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("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 #368))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #361]) #(" 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 #369)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #369] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #373))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #369] :use-brackets-p nil) #("PATH" 0 4 (:parent #374))) #("=../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 #369))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("/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 #370))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #361]) #(" which should have the same HASH values " 0 48 (:parent #371)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #371]) #("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 #375))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #371)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #371)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #371)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #381))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #382))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #371)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #371)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #386))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #387))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #371)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #389))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #390))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #371)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #371)))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((item (:standard-properties [121 121 124 156 156 0 (:tag) item nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) (plain-list (:standard-properties [121 121 121 1230 1231 1 nil planning nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) (section (:standard-properties [121 121 121 1231 1231 0 nil section nil nil nil 121 1231 nil # nil nil (headline (:standard-properties [43 43 121 1231 1231 0 (:title) nil nil nil nil 123 1229 1 # nil nil (org-data (:standard-properties [1 1 1 15256 15256 0 nil org-data nil nil nil 3 15256 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 43 43 0 nil first-section nil nil nil 1 43 nil # nil nil #20]) (keyword (:standard-properties [1 1 nil nil 43 1 nil top-comment nil nil nil nil nil nil # nil nil #23] :key "TITLE" :value "Installing GeneNetwork services"))) #15 (headline (:standard-properties [1231 1231 1247 2119 2119 0 (:title) nil nil nil nil 1249 2117 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #25))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1247 1247 1247 2119 2119 0 nil section nil nil nil 1247 2119 nil # nil nil #25]) (paragraph (:standard-properties [1247 1247 1247 1632 1633 1 nil planning nil nil nil nil nil nil # nil nil #28]) #("Large system deployments can get very " 0 38 (:parent #31)) (link (:standard-properties [1285 nil 1337 1344 1346 0 nil nil nil nil nil nil nil nil # nil nil #31] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil) #("complex" 0 7 (:parent #35))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #31)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #31] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #37))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #31))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("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 #32)) (link (:standard-properties [1851 nil 1905 1924 1927 1 nil nil nil nil nil nil nil nil # nil nil #32] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #36))) #("and " 0 4 (:parent #32)) (link (:standard-properties [1931 nil 1970 1978 1980 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #38))) #(".\n" 0 2 (:parent #32))) (paragraph (:standard-properties [1983 1983 1983 2118 2119 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #33)) (link (:standard-properties [2069 nil 2094 2114 2116 0 nil nil nil nil nil nil nil nil # nil nil #33] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #37))) #(".\n" 0 2 (:parent #33))))) (headline (:standard-properties [2119 2119 2130 2368 2368 0 (:title) nil nil nil nil 2132 2366 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 9) t] :title (#("Install" 0 7 (:parent #26))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2130 2130 2130 2368 2368 0 nil section nil nil nil 2130 2368 nil # nil nil #26]) (paragraph (:standard-properties [2130 2130 2130 2367 2368 1 nil planning nil nil nil nil nil nil # nil nil #29]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #32)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #32] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #32))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #27))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #27]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #30]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #33)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #33] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #37)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("settings.py" 0 11 (:parent #41)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #33))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #30] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #35))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #30] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #37))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #28))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #28]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #31]) #("Install redis. Make sure you add the setting:\n" 0 46 (:parent #34))) (fixed-width (:standard-properties [2913 2913 nil nil 2931 2 nil nil nil nil nil nil nil nil # nil nil #31] :value "appendonly yes")))) (headline (:standard-properties [2931 2931 2952 5782 5782 0 (:title) nil nil nil nil 2954 5780 1 # nil nil #20] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #29))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [2952 2952 2986 4250 4250 0 (:title) section nil nil nil 2988 4248 2 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #32))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2986 2986 2986 4250 4250 0 nil section nil nil nil 2986 4250 nil # nil nil #32]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #35]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #38]) #("Note: we moved to MariaDB" 0 25 (:parent #41))) #("\n" 0 1 (:parent #38))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #39))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("As root configure and run\n" 0 26 (:parent #40))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #35] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # 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nil nil #35] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #49))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("When you get errors like:\n" 0 26 (:parent #51))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("you may need to set\n" 0 20 (:parent #53))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #33))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #33]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("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 #39)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("webqtl" 0 6 (:parent #43))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("s" 0 1 (:parent #44))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #39)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("webqtl" 0 6 (:parent #46))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("plant" 0 5 (:parent #47))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #39))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("Download one database from\n" 0 27 (:parent #40))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #36]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #41))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #36]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #42))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("Check the md5sum.\n" 0 18 (:parent #43))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #44))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #36] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #46))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #36] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("and\n" 0 4 (:parent #48))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #36] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #50))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #36] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #52))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("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 #53))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("Note for the plant database you can rename it to db" 0 51 (:parent #54)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("webqtl" 0 6 (:parent #58))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("s" 0 1 (:parent #59))) #(", or\nchange the settings in etc/default" 0 39 (:parent #54)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("settings.py" 0 11 (:parent #61))) #("to match your path.\n" 0 20 (:parent #54)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #30))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #30]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #36))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #33] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #37))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #31))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #31]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("See " 0 4 (:parent #37)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #37))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #32]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #38)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #38))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #36))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #36]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #42)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("PATH" 0 4 (:parent #46))) #("and R" 0 5 (:parent #42)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("LIBS" 0 4 (:parent #48))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("SITE" 0 4 (:parent #49))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #42))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("On one system:\n" 0 15 (:parent #44))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #39] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #39]) #("and perhaps a few more.\n" 0 24 (:parent #46))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #37)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("data" 0 4 (:parent #49))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #37)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("files" 0 5 (:parent #51))) #("/genotype'" 0 10 (:parent #37))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #37]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #43)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("data" 0 4 (:parent #47))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #43)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("settings.py" 0 11 (:parent #49))) #("(see above in\nthis document).\n" 0 30 (:parent #43))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("You can use the GENENETWORK" 0 27 (:parent #44)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("FILES" 0 5 (:parent #48))) #("switch to set the datadir, for example\n" 0 39 (:parent #44))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #38))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #38]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #41]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #44))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #39))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #39]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("This error\n" 0 11 (:parent #45))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #47))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #48)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("LIBS" 0 4 (:parent #52))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("SITE" 0 4 (:parent #53))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #48))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #40))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #40]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("The following error\n" 0 20 (:parent #46))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #48))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #50))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #52)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("URI" 0 3 (:parent #56))) #("to something like\n" 0 18 (:parent #52))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #43] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #34]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #40))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("#+begin" 0 7 (:parent #41)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("src" 0 3 (:parent #45))) #("\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 #41))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #42))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #37]) #(" yes\n env GUIX" 0 30 (:parent #43)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #47))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("PATH" 0 4 (:parent #48))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #43))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("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 #44))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #37]) #(" 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 #45)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #49))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("PATH" 0 4 (:parent #50))) #("=../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 #45))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("/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 #46))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #37]) #(" which should have the same HASH values " 0 48 (:parent #47)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #47]) #("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 #51))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #47)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #47)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #47)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #57))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PATH" 0 4 (:parent #58))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #47)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #47)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #62))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PATH" 0 4 (:parent #63))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #47)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #65))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PATH" 0 4 (:parent #66))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #47)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #47))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #15))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #10)]) #5)] :type unordered) #0 (item (:standard-properties [156 156 159 181 181 0 (:tag) item nil nil nil nil nil nil # 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Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #33))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #28))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #28]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #31]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #34)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #34] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #38)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("settings.py" 0 11 (:parent #42)))) #(". 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Make sure you add the setting:\n" 0 46 (:parent #35))) (fixed-width (:standard-properties [2913 2913 nil nil 2931 2 nil nil nil nil nil nil nil nil # nil nil #32] :value "appendonly yes")))) (headline (:standard-properties [2931 2931 2952 5782 5782 0 (:title) nil nil nil nil 2954 5780 1 # nil nil #21] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #30))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [2952 2952 2986 4250 4250 0 (:title) section nil nil nil 2988 4248 2 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #33))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2986 2986 2986 4250 4250 0 nil section nil nil nil 2986 4250 nil # nil nil #33]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #36]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #39]) #("Note: we moved to MariaDB" 0 25 (:parent #42))) #("\n" 0 1 (:parent #39))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #40))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("As root configure and run\n" 0 26 (:parent #41))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #36] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # 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nil nil #36] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #50))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #36] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("When you get errors like:\n" 0 26 (:parent #52))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #36] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("you may need to set\n" 0 20 (:parent #54))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #36] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #34))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #34]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("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 #40)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("webqtl" 0 6 (:parent #44))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("s" 0 1 (:parent #45))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #40)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("webqtl" 0 6 (:parent #47))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("plant" 0 5 (:parent #48))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #40))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("Download one database from\n" 0 27 (:parent #41))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #37]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #42))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #37]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #43))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("Check the md5sum.\n" 0 18 (:parent #44))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #45))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #47))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("and\n" 0 4 (:parent #49))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #51))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #53))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("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 #54))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("Note for the plant database you can rename it to db" 0 51 (:parent #55)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("webqtl" 0 6 (:parent #59))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("s" 0 1 (:parent #60))) #(", or\nchange the settings in etc/default" 0 39 (:parent #55)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("settings.py" 0 11 (:parent #62))) #("to match your path.\n" 0 20 (:parent #55)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #31))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #31]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #37))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #34] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #38))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #32]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("See " 0 4 (:parent #38)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #38))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #33]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #39)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #39] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #39))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #37))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #37]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("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 #43)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("PATH" 0 4 (:parent #47))) #("and R" 0 5 (:parent #43)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("LIBS" 0 4 (:parent #49))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("SITE" 0 4 (:parent #50))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #43))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("On one system:\n" 0 15 (:parent #45))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #40] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #40]) #("and perhaps a few more.\n" 0 24 (:parent #47))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #38)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("data" 0 4 (:parent #50))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #38)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("files" 0 5 (:parent #52))) #("/genotype'" 0 10 (:parent #38))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #38]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #44)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("data" 0 4 (:parent #48))) #(". 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 #44)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("settings.py" 0 11 (:parent #50))) #("(see above in\nthis document).\n" 0 30 (:parent #44))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("You can use the GENENETWORK" 0 27 (:parent #45)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("FILES" 0 5 (:parent #49))) #("switch to set the datadir, for example\n" 0 39 (:parent #45))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #39))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #39]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #42]) #("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 #45))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #40))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #40]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("This error\n" 0 11 (:parent #46))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("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 #48))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #49)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("LIBS" 0 4 (:parent #53))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("SITE" 0 4 (:parent #54))) #(". 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 #49))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #41))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #41]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("The following error\n" 0 20 (:parent #47))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("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 #49))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #51))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #53)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("URI" 0 3 (:parent #57))) #("to something like\n" 0 18 (:parent #53))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #44] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #35]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #41))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("#+begin" 0 7 (:parent #42)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("src" 0 3 (:parent #46))) #("\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 #42))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #43))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #38]) #(" yes\n env GUIX" 0 30 (:parent #44)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #48))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("PATH" 0 4 (:parent #49))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #44))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("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 #45))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #38]) #(" 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 #46)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #50))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("PATH" 0 4 (:parent #51))) #("=../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 #46))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("/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 #47))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #38]) #(" which should have the same HASH values " 0 48 (:parent #48)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #48]) #("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 #52))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #48)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #48)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #48] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #48)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #58))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PATH" 0 4 (:parent #59))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #48)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #48)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #63))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PATH" 0 4 (:parent #64))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #48)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #66))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PATH" 0 4 (:parent #67))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #48)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #48))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #16))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #11)]) #6)] :type unordered) . #0)] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [124 124 124 156 156 0 nil nil nil nil nil nil nil nil # nil nil #1]) (link (:standard-properties [124 nil 141 153 155 0 nil nil nil nil nil nil nil nil # nil nil #4] :type "custom-id" :type-explicit-p nil :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil) #("Introduction" 0 12 (:parent #7))) #("\n" 0 1 (:parent #4)))) (item (:standard-properties [156 156 159 181 181 0 (:tag) item nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) (plain-list (:standard-properties [121 121 121 1230 1231 1 nil planning nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) (section (:standard-properties [121 121 121 1231 1231 0 nil section nil nil nil 121 1231 nil # nil nil (headline (:standard-properties [43 43 121 1231 1231 0 (:title) nil nil nil nil 123 1229 1 # nil nil (org-data (:standard-properties [1 1 1 15256 15256 0 nil org-data nil nil nil 3 15256 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 43 43 0 nil first-section nil nil nil 1 43 nil # nil nil #22]) (keyword (:standard-properties [1 1 nil nil 43 1 nil top-comment nil nil nil nil nil nil # nil nil #25] :key "TITLE" :value "Installing GeneNetwork services"))) #17 (headline (:standard-properties [1231 1231 1247 2119 2119 0 (:title) nil nil nil nil 1249 2117 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #27))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1247 1247 1247 2119 2119 0 nil section nil nil nil 1247 2119 nil # nil nil #27]) (paragraph (:standard-properties [1247 1247 1247 1632 1633 1 nil planning nil nil nil nil nil nil # nil nil #30]) #("Large system deployments can get very " 0 38 (:parent #33)) (link (:standard-properties [1285 nil 1337 1344 1346 0 nil nil nil nil nil nil nil nil # nil nil #33] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil) #("complex" 0 7 (:parent #37))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #33)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #33] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #39))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #33))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #34)) (link (:standard-properties [1851 nil 1905 1924 1927 1 nil nil nil nil nil nil nil nil # nil nil #34] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #38))) #("and " 0 4 (:parent #34)) (link (:standard-properties [1931 nil 1970 1978 1980 0 nil nil nil nil nil nil nil nil # nil nil #34] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #40))) #(".\n" 0 2 (:parent #34))) (paragraph (:standard-properties [1983 1983 1983 2118 2119 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #35)) (link (:standard-properties [2069 nil 2094 2114 2116 0 nil nil nil nil nil nil nil nil # nil nil #35] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #39))) #(".\n" 0 2 (:parent #35))))) (headline (:standard-properties [2119 2119 2130 2368 2368 0 (:title) nil nil nil nil 2132 2366 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 9) t] :title (#("Install" 0 7 (:parent #28))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2130 2130 2130 2368 2368 0 nil section nil nil nil 2130 2368 nil # nil nil #28]) (paragraph (:standard-properties [2130 2130 2130 2367 2368 1 nil planning nil nil nil nil nil nil # nil nil #31]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #34)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #34] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #34))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #29))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #29]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #32]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #35)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #35] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #39)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("settings.py" 0 11 (:parent #43)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #35))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #32] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #37))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #32] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #39))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #30))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #30]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("Install redis. Make sure you add the setting:\n" 0 46 (:parent #36))) (fixed-width (:standard-properties [2913 2913 nil nil 2931 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "appendonly yes")))) (headline (:standard-properties [2931 2931 2952 5782 5782 0 (:title) nil nil nil nil 2954 5780 1 # nil nil #22] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #31))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [2952 2952 2986 4250 4250 0 (:title) section nil nil nil 2988 4248 2 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #34))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2986 2986 2986 4250 4250 0 nil section nil nil nil 2986 4250 nil # nil nil #34]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #37]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #40]) #("Note: we moved to MariaDB" 0 25 (:parent #43))) #("\n" 0 1 (:parent #40))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #41))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("As root configure and run\n" 0 26 (:parent #42))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #37] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # 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nil nil #37] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #51))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("When you get errors like:\n" 0 26 (:parent #53))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("you may need to set\n" 0 20 (:parent #55))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #35))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #35]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("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 #41)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("webqtl" 0 6 (:parent #45))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("s" 0 1 (:parent #46))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #41)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("webqtl" 0 6 (:parent #48))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("plant" 0 5 (:parent #49))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #41))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Download one database from\n" 0 27 (:parent #42))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #38]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #43))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #38]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #44))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Check the md5sum.\n" 0 18 (:parent #45))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #46))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #48))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("and\n" 0 4 (:parent #50))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #52))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #54))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #55))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Note for the plant database you can rename it to db" 0 51 (:parent #56)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("webqtl" 0 6 (:parent #60))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("s" 0 1 (:parent #61))) #(", or\nchange the settings in etc/default" 0 39 (:parent #56)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("settings.py" 0 11 (:parent #63))) #("to match your path.\n" 0 20 (:parent #56)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #32]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #38))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #35] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #39] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #39))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #33]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("See " 0 4 (:parent #39)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #39] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #39))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #34]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #40)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #40] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #40))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #35] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #38))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #38]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("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 #44)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("PATH" 0 4 (:parent #48))) #("and R" 0 5 (:parent #44)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("LIBS" 0 4 (:parent #50))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("SITE" 0 4 (:parent #51))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #44))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("On one system:\n" 0 15 (:parent #46))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #41] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #41]) #("and perhaps a few more.\n" 0 24 (:parent #48))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #35] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #39)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("data" 0 4 (:parent #51))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #39)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("files" 0 5 (:parent #53))) #("/genotype'" 0 10 (:parent #39))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #39]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #45)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("data" 0 4 (:parent #49))) #(". 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 #45)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("settings.py" 0 11 (:parent #51))) #("(see above in\nthis document).\n" 0 30 (:parent #45))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("You can use the GENENETWORK" 0 27 (:parent #46)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("FILES" 0 5 (:parent #50))) #("switch to set the datadir, for example\n" 0 39 (:parent #46))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #35] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #40))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #40]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #43]) #("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 #46))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #35] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #41))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #41]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("This error\n" 0 11 (:parent #47))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("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 #49))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #50)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("LIBS" 0 4 (:parent #54))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("SITE" 0 4 (:parent #55))) #(". 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 #50))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #35] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #42))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #42]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("The following error\n" 0 20 (:parent #48))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("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 #50))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #52))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #54)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("URI" 0 3 (:parent #58))) #("to something like\n" 0 18 (:parent #54))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #45] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #36]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #42))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("#+begin" 0 7 (:parent #43)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("src" 0 3 (:parent #47))) #("\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 #43))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #44))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #39]) #(" yes\n env GUIX" 0 30 (:parent #45)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #49))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("PATH" 0 4 (:parent #50))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #45))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("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 #46))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #39]) #(" 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 #47)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #51))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PATH" 0 4 (:parent #52))) #("=../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 #47))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("/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 #48))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #39]) #(" which should have the same HASH values " 0 48 (:parent #49)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #49]) #("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 #53))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #49)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #49)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #49] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #49)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #59))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PATH" 0 4 (:parent #60))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #49)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #49)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #64))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PATH" 0 4 (:parent #65))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #49)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #67))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PATH" 0 4 (:parent #68))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #49)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #49))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #17))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #12)]) #7)] :type unordered) . #0)] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [159 159 159 181 181 0 nil nil nil nil nil nil nil nil # nil nil #2]) (link (:standard-properties [159 nil 171 178 180 0 nil nil nil nil nil nil nil nil # nil nil #5] :type "custom-id" :type-explicit-p nil :path "install" :format bracket :raw-link "#install" :application nil :search-option nil) #("Install" 0 7 (:parent #8))) #("\n" 0 1 (:parent #5)))) (item (:standard-properties [181 181 184 214 214 0 (:tag) item nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) (plain-list (:standard-properties [121 121 121 1230 1231 1 nil planning nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) (section (:standard-properties [121 121 121 1231 1231 0 nil section nil nil nil 121 1231 nil # nil nil (headline (:standard-properties [43 43 121 1231 1231 0 (:title) nil nil nil nil 123 1229 1 # nil nil (org-data (:standard-properties [1 1 1 15256 15256 0 nil org-data nil nil nil 3 15256 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 43 43 0 nil first-section nil nil nil 1 43 nil # nil nil #23]) (keyword (:standard-properties [1 1 nil nil 43 1 nil top-comment nil nil nil nil nil nil # nil nil #26] :key "TITLE" :value "Installing GeneNetwork services"))) #18 (headline (:standard-properties [1231 1231 1247 2119 2119 0 (:title) nil nil nil nil 1249 2117 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #28))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1247 1247 1247 2119 2119 0 nil section nil nil nil 1247 2119 nil # nil nil #28]) (paragraph (:standard-properties [1247 1247 1247 1632 1633 1 nil planning nil nil nil nil nil nil # nil nil #31]) #("Large system deployments can get very " 0 38 (:parent #34)) (link (:standard-properties [1285 nil 1337 1344 1346 0 nil nil nil nil nil nil nil nil # nil nil #34] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil) #("complex" 0 7 (:parent #38))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #34)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #34] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #40))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #34))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #35)) (link (:standard-properties [1851 nil 1905 1924 1927 1 nil nil nil nil nil nil nil nil # nil nil #35] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #39))) #("and " 0 4 (:parent #35)) (link (:standard-properties [1931 nil 1970 1978 1980 0 nil nil nil nil nil nil nil nil # nil nil #35] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #41))) #(".\n" 0 2 (:parent #35))) (paragraph (:standard-properties [1983 1983 1983 2118 2119 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #36)) (link (:standard-properties [2069 nil 2094 2114 2116 0 nil nil nil nil nil nil nil nil # nil nil #36] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #40))) #(".\n" 0 2 (:parent #36))))) (headline (:standard-properties [2119 2119 2130 2368 2368 0 (:title) nil nil nil nil 2132 2366 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 9) t] :title (#("Install" 0 7 (:parent #29))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2130 2130 2130 2368 2368 0 nil section nil nil nil 2130 2368 nil # nil nil #29]) (paragraph (:standard-properties [2130 2130 2130 2367 2368 1 nil planning nil nil nil nil nil nil # nil nil #32]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #35)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #35] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #35))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #30))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #30]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #36)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #36] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #40)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("settings.py" 0 11 (:parent #44)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #36))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #38))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #40))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #31))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #31]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("Install redis. Make sure you add the setting:\n" 0 46 (:parent #37))) (fixed-width (:standard-properties [2913 2913 nil nil 2931 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "appendonly yes")))) (headline (:standard-properties [2931 2931 2952 5782 5782 0 (:title) nil nil nil nil 2954 5780 1 # nil nil #23] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [2952 2952 2986 4250 4250 0 (:title) section nil nil nil 2988 4248 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #35))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2986 2986 2986 4250 4250 0 nil section nil nil nil 2986 4250 nil # nil nil #35]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #38]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #41]) #("Note: we moved to MariaDB" 0 25 (:parent #44))) #("\n" 0 1 (:parent #41))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #42))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("As root configure and run\n" 0 26 (:parent #43))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #38] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # 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nil nil #38] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #52))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("When you get errors like:\n" 0 26 (:parent #54))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # 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Currently we have two databases for deployment,\n'db" 0 163 (:parent #42)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("webqtl" 0 6 (:parent #46))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("s" 0 1 (:parent #47))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #42)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("webqtl" 0 6 (:parent #49))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("plant" 0 5 (:parent #50))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #42))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Download one database from\n" 0 27 (:parent #43))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #39]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #44))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #39]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #45))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Check the md5sum.\n" 0 18 (:parent #46))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #47))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #49))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("and\n" 0 4 (:parent #51))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #53))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #55))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #56))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Note for the plant database you can rename it to db" 0 51 (:parent #57)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("webqtl" 0 6 (:parent #61))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("s" 0 1 (:parent #62))) #(", or\nchange the settings in etc/default" 0 39 (:parent #57)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("settings.py" 0 11 (:parent #64))) #("to match your path.\n" 0 20 (:parent #57)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #33]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #39))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #36] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #40] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #40))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #34]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("See " 0 4 (:parent #40)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #40] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #40))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #35]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #41)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #41))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #36] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #39))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #39]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("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 #45)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("PATH" 0 4 (:parent #49))) #("and R" 0 5 (:parent #45)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("LIBS" 0 4 (:parent #51))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("SITE" 0 4 (:parent #52))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #45))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("On one system:\n" 0 15 (:parent #47))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #42] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #42]) #("and perhaps a few more.\n" 0 24 (:parent #49))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #36] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #40)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("data" 0 4 (:parent #52))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #40)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("files" 0 5 (:parent #54))) #("/genotype'" 0 10 (:parent #40))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #40]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #46)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("data" 0 4 (:parent #50))) #(". 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 #46)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("settings.py" 0 11 (:parent #52))) #("(see above in\nthis document).\n" 0 30 (:parent #46))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("You can use the GENENETWORK" 0 27 (:parent #47)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("FILES" 0 5 (:parent #51))) #("switch to set the datadir, for example\n" 0 39 (:parent #47))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #36] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #41))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #41]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #44]) #("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 #47))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #36] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #42))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #42]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("This error\n" 0 11 (:parent #48))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("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 #50))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #51)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("LIBS" 0 4 (:parent #55))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("SITE" 0 4 (:parent #56))) #(". 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 #51))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #36] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #43))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #43]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("The following error\n" 0 20 (:parent #49))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("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 #51))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #53))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #55)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("URI" 0 3 (:parent #59))) #("to something like\n" 0 18 (:parent #55))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #46] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #37]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #43))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("#+begin" 0 7 (:parent #44)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("src" 0 3 (:parent #48))) #("\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 #44))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #45))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #40]) #(" yes\n env GUIX" 0 30 (:parent #46)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #50))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("PATH" 0 4 (:parent #51))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #46))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("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 #47))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #40]) #(" 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 #48)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #52))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PATH" 0 4 (:parent #53))) #("=../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 #48))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("/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 #49))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #40]) #(" which should have the same HASH values " 0 48 (:parent #50)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #50]) #("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 #54))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #50)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #50] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #50)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #50] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #50)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #60))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PATH" 0 4 (:parent #61))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #50)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #50] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #50)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #65))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PATH" 0 4 (:parent #66))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #50)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #68))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PATH" 0 4 (:parent #69))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #50)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #50] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #50))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #18))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #13)]) #8)] :type unordered) . #0)] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [184 184 184 214 214 0 nil nil nil nil nil nil nil nil # nil nil #3]) (link (:standard-properties [184 nil 200 211 213 0 nil nil nil nil nil nil nil nil # nil nil #6] :type "custom-id" :type-explicit-p nil :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil) #("Running GN2" 0 11 (:parent #9))) #("\n" 0 1 (:parent #6)))) (item (:standard-properties [214 214 217 409 409 0 (:tag) item nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) (plain-list (:standard-properties [121 121 121 1230 1231 1 nil planning nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) (section (:standard-properties [121 121 121 1231 1231 0 nil section nil nil nil 121 1231 nil # nil nil (headline (:standard-properties [43 43 121 1231 1231 0 (:title) nil nil nil nil 123 1229 1 # nil nil (org-data (:standard-properties [1 1 1 15256 15256 0 nil org-data nil nil nil 3 15256 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 43 43 0 nil first-section nil nil nil 1 43 nil # nil nil #24]) (keyword (:standard-properties [1 1 nil nil 43 1 nil top-comment nil nil nil nil nil nil # nil nil #27] :key "TITLE" :value "Installing GeneNetwork services"))) #19 (headline (:standard-properties [1231 1231 1247 2119 2119 0 (:title) nil nil nil nil 1249 2117 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #29))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1247 1247 1247 2119 2119 0 nil section nil nil nil 1247 2119 nil # nil nil #29]) (paragraph (:standard-properties [1247 1247 1247 1632 1633 1 nil planning nil nil nil nil nil nil # nil nil #32]) #("Large system deployments can get very " 0 38 (:parent #35)) (link (:standard-properties [1285 nil 1337 1344 1346 0 nil nil nil nil nil nil nil nil # nil nil #35] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil) #("complex" 0 7 (:parent #39))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #35)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #35] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #41))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #35))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("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 #36)) (link (:standard-properties [1851 nil 1905 1924 1927 1 nil nil nil nil nil nil nil nil # nil nil #36] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #40))) #("and " 0 4 (:parent #36)) (link (:standard-properties [1931 nil 1970 1978 1980 0 nil nil nil nil nil nil nil nil # nil nil #36] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #42))) #(".\n" 0 2 (:parent #36))) (paragraph (:standard-properties [1983 1983 1983 2118 2119 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #37)) (link (:standard-properties [2069 nil 2094 2114 2116 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #41))) #(".\n" 0 2 (:parent #37))))) (headline (:standard-properties [2119 2119 2130 2368 2368 0 (:title) nil nil nil nil 2132 2366 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 9) t] :title (#("Install" 0 7 (:parent #30))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2130 2130 2130 2368 2368 0 nil section nil nil nil 2130 2368 nil # nil nil #30]) (paragraph (:standard-properties [2130 2130 2130 2367 2368 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #36)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #36] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #36))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #31))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #31]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #37)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #41)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("settings.py" 0 11 (:parent #45)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #37))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #39))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #41))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #32]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("Install redis. Make sure you add the setting:\n" 0 46 (:parent #38))) (fixed-width (:standard-properties [2913 2913 nil nil 2931 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "appendonly yes")))) (headline (:standard-properties [2931 2931 2952 5782 5782 0 (:title) nil nil nil nil 2954 5780 1 # nil nil #24] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [2952 2952 2986 4250 4250 0 (:title) section nil nil nil 2988 4248 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #36))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2986 2986 2986 4250 4250 0 nil section nil nil nil 2986 4250 nil # nil nil #36]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #39]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #42]) #("Note: we moved to MariaDB" 0 25 (:parent #45))) #("\n" 0 1 (:parent #42))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #43))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("As root configure and run\n" 0 26 (:parent #44))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #39] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # 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nil nil #39] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #53))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("When you get errors like:\n" 0 26 (:parent #55))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("you may need to set\n" 0 20 (:parent #57))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #37))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #37]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #43)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("webqtl" 0 6 (:parent #47))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("s" 0 1 (:parent #48))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #43)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("webqtl" 0 6 (:parent #50))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("plant" 0 5 (:parent #51))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #43))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Download one database from\n" 0 27 (:parent #44))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #40]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #45))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #40]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #46))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Check the md5sum.\n" 0 18 (:parent #47))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #48))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #50))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("and\n" 0 4 (:parent #52))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #54))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #56))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #57))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Note for the plant database you can rename it to db" 0 51 (:parent #58)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("webqtl" 0 6 (:parent #62))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("s" 0 1 (:parent #63))) #(", or\nchange the settings in etc/default" 0 39 (:parent #58)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("settings.py" 0 11 (:parent #65))) #("to match your path.\n" 0 20 (:parent #58)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #34]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #40))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #37] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #41))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #35]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("See " 0 4 (:parent #41)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #41))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #36]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #42)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #42))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #40))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #40]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #46)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("PATH" 0 4 (:parent #50))) #("and R" 0 5 (:parent #46)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("LIBS" 0 4 (:parent #52))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("SITE" 0 4 (:parent #53))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #46))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("On one system:\n" 0 15 (:parent #48))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #43] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #43]) #("and perhaps a few more.\n" 0 24 (:parent #50))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #41)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("data" 0 4 (:parent #53))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #41)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("files" 0 5 (:parent #55))) #("/genotype'" 0 10 (:parent #41))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #41]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #47)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("data" 0 4 (:parent #51))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #47)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("settings.py" 0 11 (:parent #53))) #("(see above in\nthis document).\n" 0 30 (:parent #47))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("You can use the GENENETWORK" 0 27 (:parent #48)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("FILES" 0 5 (:parent #52))) #("switch to set the datadir, for example\n" 0 39 (:parent #48))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #42))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #42]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #45]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #48))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #43))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #43]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("This error\n" 0 11 (:parent #49))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #51))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #52)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("LIBS" 0 4 (:parent #56))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("SITE" 0 4 (:parent #57))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #52))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #44))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #44]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("The following error\n" 0 20 (:parent #50))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #52))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #54))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #56)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("URI" 0 3 (:parent #60))) #("to something like\n" 0 18 (:parent #56))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #47] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #38]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #44))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("#+begin" 0 7 (:parent #45)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("src" 0 3 (:parent #49))) #("\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 #45))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #46))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #41]) #(" yes\n env GUIX" 0 30 (:parent #47)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #51))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PATH" 0 4 (:parent #52))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #47))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #48))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #41]) #(" 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 #49)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #53))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PATH" 0 4 (:parent #54))) #("=../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 #49))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("/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 #50))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #41]) #(" which should have the same HASH values " 0 48 (:parent #51)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #51]) #("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 #55))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #51)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #51)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #51] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #51)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #61))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PATH" 0 4 (:parent #62))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #51)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #51)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #66))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PATH" 0 4 (:parent #67))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #51)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #69))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PATH" 0 4 (:parent #70))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #51)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #51))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #19))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #14)]) #9)] :type unordered) . #0)] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [217 217 217 261 261 0 nil nil nil nil nil nil nil nil # nil nil #4]) (link (:standard-properties [217 nil 240 258 260 0 nil nil nil nil nil nil nil nil # nil nil #7] :type "custom-id" :type-explicit-p nil :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil) #("Run MariaDB server" 0 18 (:parent #10))) #("\n" 0 1 (:parent #7))) (plain-list (:standard-properties [261 261 261 409 409 0 nil nil nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) #4] :type unordered) (item (:standard-properties [261 261 266 332 332 0 (:tag) item nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) #8] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [266 266 266 332 332 0 nil nil nil nil nil nil nil nil # nil nil #11]) (link (:standard-properties [266 nil 300 329 331 0 nil nil nil nil nil nil nil nil # nil nil #14] :type "custom-id" :type-explicit-p nil :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil) #("Install MariaDB with GNU GUIx" 0 29 (:parent #17))) #("\n" 0 1 (:parent #14)))) (item (:standard-properties [332 332 337 409 409 0 (:tag) item nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) #8] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [337 337 337 409 409 0 nil nil nil nil nil nil nil nil # nil nil #12]) (link (:standard-properties [337 nil 374 406 408 0 nil nil nil nil nil nil nil nil # nil nil #15] :type "custom-id" :type-explicit-p nil :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil) #("Load the small database in MySQL" 0 32 (:parent #18))) #("\n" 0 1 (:parent #15)))))) (item (:standard-properties [409 409 412 460 460 0 (:tag) item nil nil nil nil nil nil # 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nil nil #30]) (paragraph (:standard-properties [1247 1247 1247 1632 1633 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("Large system deployments can get very " 0 38 (:parent #36)) (link (:standard-properties [1285 nil 1337 1344 1346 0 nil nil nil nil nil nil nil nil # nil nil #36] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil) #("complex" 0 7 (:parent #40))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #36)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #36] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #42))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #36))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #37)) (link (:standard-properties [1851 nil 1905 1924 1927 1 nil nil nil nil nil nil nil nil # nil nil #37] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #41))) #("and " 0 4 (:parent #37)) (link (:standard-properties [1931 nil 1970 1978 1980 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #43))) #(".\n" 0 2 (:parent #37))) (paragraph (:standard-properties [1983 1983 1983 2118 2119 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #38)) (link (:standard-properties [2069 nil 2094 2114 2116 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #42))) #(".\n" 0 2 (:parent #38))))) (headline (:standard-properties [2119 2119 2130 2368 2368 0 (:title) nil nil nil nil 2132 2366 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 9) t] :title (#("Install" 0 7 (:parent #31))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2130 2130 2130 2368 2368 0 nil section nil nil nil 2130 2368 nil # nil nil #31]) (paragraph (:standard-properties [2130 2130 2130 2367 2368 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #37)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #37] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #37))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #32]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #38)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #42)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("settings.py" 0 11 (:parent #46)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #38))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #40))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #42))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #33]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("Install redis. Make sure you add the setting:\n" 0 46 (:parent #39))) (fixed-width (:standard-properties [2913 2913 nil nil 2931 2 nil nil nil nil nil nil nil nil # nil nil #36] :value "appendonly yes")))) (headline (:standard-properties [2931 2931 2952 5782 5782 0 (:title) nil nil nil nil 2954 5780 1 # nil nil #25] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [2952 2952 2986 4250 4250 0 (:title) section nil nil nil 2988 4248 2 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #37))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2986 2986 2986 4250 4250 0 nil section nil nil nil 2986 4250 nil # nil nil #37]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #40]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #43]) #("Note: we moved to MariaDB" 0 25 (:parent #46))) #("\n" 0 1 (:parent #43))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #44))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("As root configure and run\n" 0 26 (:parent #45))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #40] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # 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nil nil #40] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #54))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("When you get errors like:\n" 0 26 (:parent #56))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # 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Currently we have two databases for deployment,\n'db" 0 163 (:parent #44)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("webqtl" 0 6 (:parent #48))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("s" 0 1 (:parent #49))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #44)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("webqtl" 0 6 (:parent #51))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("plant" 0 5 (:parent #52))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #44))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Download one database from\n" 0 27 (:parent #45))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #41]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #46))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #41]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #47))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Check the md5sum.\n" 0 18 (:parent #48))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #49))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #51))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("and\n" 0 4 (:parent #53))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #55))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #57))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #58))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Note for the plant database you can rename it to db" 0 51 (:parent #59)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("webqtl" 0 6 (:parent #63))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("s" 0 1 (:parent #64))) #(", or\nchange the settings in etc/default" 0 39 (:parent #59)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("settings.py" 0 11 (:parent #66))) #("to match your path.\n" 0 20 (:parent #59)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #35]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #41))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #38] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #42))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #36]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("See " 0 4 (:parent #42)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #42))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #37]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #43)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #43))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #41))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #41]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #47)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PATH" 0 4 (:parent #51))) #("and R" 0 5 (:parent #47)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("LIBS" 0 4 (:parent #53))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("SITE" 0 4 (:parent #54))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #47))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("On one system:\n" 0 15 (:parent #49))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #44] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #44]) #("and perhaps a few more.\n" 0 24 (:parent #51))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #42)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("data" 0 4 (:parent #54))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #42)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("files" 0 5 (:parent #56))) #("/genotype'" 0 10 (:parent #42))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #42]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #48)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("data" 0 4 (:parent #52))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #48)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("settings.py" 0 11 (:parent #54))) #("(see above in\nthis document).\n" 0 30 (:parent #48))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("You can use the GENENETWORK" 0 27 (:parent #49)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("FILES" 0 5 (:parent #53))) #("switch to set the datadir, for example\n" 0 39 (:parent #49))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #43))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #43]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #46]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #49))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #44))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #44]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("This error\n" 0 11 (:parent #50))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("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 #52))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #53)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("LIBS" 0 4 (:parent #57))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("SITE" 0 4 (:parent #58))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #53))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #45]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("The following error\n" 0 20 (:parent #51))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #53))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #55))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #57)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("URI" 0 3 (:parent #61))) #("to something like\n" 0 18 (:parent #57))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #48] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #39]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #45))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("#+begin" 0 7 (:parent #46)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("src" 0 3 (:parent #50))) #("\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 #46))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #47))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #42]) #(" yes\n env GUIX" 0 30 (:parent #48)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #52))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PATH" 0 4 (:parent #53))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #48))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #49))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #42]) #(" 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 #50)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #54))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PATH" 0 4 (:parent #55))) #("=../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 #50))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("/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 #51))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #42]) #(" which should have the same HASH values " 0 48 (:parent #52)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #52]) #("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 #56))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #52)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #52)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #52)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #62))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PATH" 0 4 (:parent #63))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #52)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #52)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #67))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PATH" 0 4 (:parent #68))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #52)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #70))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PATH" 0 4 (:parent #71))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #52)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #52))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #20))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #15)]) #10)] :type unordered) . #0)] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [412 412 412 460 460 0 nil nil nil nil nil nil nil nil # nil nil #5]) (link (:standard-properties [412 nil 437 457 459 0 nil nil nil nil nil nil nil nil # nil nil #8] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #11))) #("\n" 0 1 (:parent #8)))) (item (:standard-properties [460 460 463 535 535 0 (:tag) item nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) (plain-list (:standard-properties [121 121 121 1230 1231 1 nil planning nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) (section (:standard-properties [121 121 121 1231 1231 0 nil section nil nil nil 121 1231 nil # nil nil (headline (:standard-properties [43 43 121 1231 1231 0 (:title) nil nil nil nil 123 1229 1 # nil nil (org-data (:standard-properties [1 1 1 15256 15256 0 nil org-data nil nil nil 3 15256 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 43 43 0 nil first-section nil nil nil 1 43 nil # nil nil #26]) (keyword (:standard-properties [1 1 nil nil 43 1 nil top-comment nil nil nil nil nil nil # nil nil #29] :key "TITLE" :value "Installing GeneNetwork services"))) #21 (headline (:standard-properties [1231 1231 1247 2119 2119 0 (:title) nil nil nil nil 1249 2117 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #31))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1247 1247 1247 2119 2119 0 nil section nil nil nil 1247 2119 nil # nil nil #31]) (paragraph (:standard-properties [1247 1247 1247 1632 1633 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("Large system deployments can get very " 0 38 (:parent #37)) (link (:standard-properties [1285 nil 1337 1344 1346 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil) #("complex" 0 7 (:parent #41))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #37)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #43))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #37))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #38)) (link (:standard-properties [1851 nil 1905 1924 1927 1 nil nil nil nil nil nil nil nil # nil nil #38] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #42))) #("and " 0 4 (:parent #38)) (link (:standard-properties [1931 nil 1970 1978 1980 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #44))) #(".\n" 0 2 (:parent #38))) (paragraph (:standard-properties [1983 1983 1983 2118 2119 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #39)) (link (:standard-properties [2069 nil 2094 2114 2116 0 nil nil nil nil nil nil nil nil # nil nil #39] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #43))) #(".\n" 0 2 (:parent #39))))) (headline (:standard-properties [2119 2119 2130 2368 2368 0 (:title) nil nil nil nil 2132 2366 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 9) t] :title (#("Install" 0 7 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2130 2130 2130 2368 2368 0 nil section nil nil nil 2130 2368 nil # nil nil #32]) (paragraph (:standard-properties [2130 2130 2130 2367 2368 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #38)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #38] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #38))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #33]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #39)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #39] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #43)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("settings.py" 0 11 (:parent #47)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #39))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #36] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #41))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #36] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #43))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #34]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("Install redis. Make sure you add the setting:\n" 0 46 (:parent #40))) (fixed-width (:standard-properties [2913 2913 nil nil 2931 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "appendonly yes")))) (headline (:standard-properties [2931 2931 2952 5782 5782 0 (:title) nil nil nil nil 2954 5780 1 # nil nil #26] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [2952 2952 2986 4250 4250 0 (:title) section nil nil nil 2988 4248 2 # nil nil #35] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #38))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2986 2986 2986 4250 4250 0 nil section nil nil nil 2986 4250 nil # nil nil #38]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #41]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #44]) #("Note: we moved to MariaDB" 0 25 (:parent #47))) #("\n" 0 1 (:parent #44))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #45))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("As root configure and run\n" 0 26 (:parent #46))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #41] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("If you want to run as root you may have to set\n" 0 47 (:parent #48))) (fixed-width (:standard-properties [3523 3523 nil nil 3563 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [3563 3563 3563 3584 3585 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("You also need to set\n" 0 21 (:parent #50))) (fixed-width (:standard-properties [3585 3585 nil nil 3608 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [3608 3608 3608 3687 3688 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #52))) (paragraph (:standard-properties [3688 3688 3688 3756 3757 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #53))) (fixed-width (:standard-properties [3757 3757 nil nil 3872 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #55))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("When you get errors like:\n" 0 26 (:parent #57))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("you may need to set\n" 0 20 (:parent #59))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #35] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #39))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #39]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #45)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("webqtl" 0 6 (:parent #49))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("s" 0 1 (:parent #50))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #45)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("webqtl" 0 6 (:parent #52))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("plant" 0 5 (:parent #53))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #45))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Download one database from\n" 0 27 (:parent #46))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #42]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #47))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #42]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #48))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Check the md5sum.\n" 0 18 (:parent #49))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #50))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #52))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("and\n" 0 4 (:parent #54))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #56))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #58))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #59))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Note for the plant database you can rename it to db" 0 51 (:parent #60)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #60] :use-brackets-p nil) #("webqtl" 0 6 (:parent #64))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #60] :use-brackets-p nil) #("s" 0 1 (:parent #65))) #(", or\nchange the settings in etc/default" 0 39 (:parent #60)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #60] :use-brackets-p nil) #("settings.py" 0 11 (:parent #67))) #("to match your path.\n" 0 20 (:parent #60)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #36]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #42))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #39] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #43))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #37]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("See " 0 4 (:parent #43)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #43))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #38]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #44)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #44))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #42))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #42]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #48)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PATH" 0 4 (:parent #52))) #("and R" 0 5 (:parent #48)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("LIBS" 0 4 (:parent #54))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("SITE" 0 4 (:parent #55))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #48))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("On one system:\n" 0 15 (:parent #50))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #45] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #45]) #("and perhaps a few more.\n" 0 24 (:parent #52))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #43)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("data" 0 4 (:parent #55))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #43)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("files" 0 5 (:parent #57))) #("/genotype'" 0 10 (:parent #43))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #43]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #49)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("data" 0 4 (:parent #53))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #49)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("settings.py" 0 11 (:parent #55))) #("(see above in\nthis document).\n" 0 30 (:parent #49))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("You can use the GENENETWORK" 0 27 (:parent #50)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("FILES" 0 5 (:parent #54))) #("switch to set the datadir, for example\n" 0 39 (:parent #50))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #44))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #44]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #47]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #50))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #45]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("This error\n" 0 11 (:parent #51))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #53))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #54)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("LIBS" 0 4 (:parent #58))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("SITE" 0 4 (:parent #59))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #54))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #46]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("The following error\n" 0 20 (:parent #52))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #54))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #56))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #58)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("URI" 0 3 (:parent #62))) #("to something like\n" 0 18 (:parent #58))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #49] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #40]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #46))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("#+begin" 0 7 (:parent #47)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("src" 0 3 (:parent #51))) #("\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 #47))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #48))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #43]) #(" yes\n env GUIX" 0 30 (:parent #49)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #53))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PATH" 0 4 (:parent #54))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #49))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("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 #50))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #43]) #(" 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 #51)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #55))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PATH" 0 4 (:parent #56))) #("=../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 #51))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("/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 #52))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #43]) #(" which should have the same HASH values " 0 48 (:parent #53)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #53]) #("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 #57))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #53)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #53)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #53] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #53)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #63))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PATH" 0 4 (:parent #64))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #53)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #53)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #68))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PATH" 0 4 (:parent #69))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #53)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #71))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PATH" 0 4 (:parent #72))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #53)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #53))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #21))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #16)]) #11)] :type unordered) . #0)] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [463 463 463 535 535 0 nil nil nil nil nil nil nil nil # nil nil #6]) (link (:standard-properties [463 nil 500 532 534 0 nil nil nil nil nil nil nil nil # nil nil #9] :type "custom-id" :type-explicit-p nil :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil) #("Working with the GN2 source code" 0 32 (:parent #12))) #("\n" 0 1 (:parent #9)))) (item (:standard-properties [535 535 538 564 564 0 (:tag) item nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) (plain-list (:standard-properties [121 121 121 1230 1231 1 nil planning nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) (section (:standard-properties [121 121 121 1231 1231 0 nil section nil nil nil 121 1231 nil # nil nil (headline (:standard-properties [43 43 121 1231 1231 0 (:title) nil nil nil nil 123 1229 1 # nil nil (org-data (:standard-properties [1 1 1 15256 15256 0 nil org-data nil nil nil 3 15256 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 43 43 0 nil first-section nil nil nil 1 43 nil # nil nil #27]) (keyword (:standard-properties [1 1 nil nil 43 1 nil top-comment nil nil nil nil nil nil # nil nil #30] :key "TITLE" :value "Installing GeneNetwork services"))) #22 (headline (:standard-properties [1231 1231 1247 2119 2119 0 (:title) nil nil nil nil 1249 2117 1 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1247 1247 1247 2119 2119 0 nil section nil nil nil 1247 2119 nil # nil nil #32]) (paragraph (:standard-properties [1247 1247 1247 1632 1633 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("Large system deployments can get very " 0 38 (:parent #38)) (link (:standard-properties [1285 nil 1337 1344 1346 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil) #("complex" 0 7 (:parent #42))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #38)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #44))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #38))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("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 #39)) (link (:standard-properties [1851 nil 1905 1924 1927 1 nil nil nil nil nil nil nil nil # nil nil #39] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #43))) #("and " 0 4 (:parent #39)) (link (:standard-properties [1931 nil 1970 1978 1980 0 nil nil nil nil nil nil nil nil # nil nil #39] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #45))) #(".\n" 0 2 (:parent #39))) (paragraph (:standard-properties [1983 1983 1983 2118 2119 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #40)) (link (:standard-properties [2069 nil 2094 2114 2116 0 nil nil nil nil nil nil nil nil # nil nil #40] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #44))) #(".\n" 0 2 (:parent #40))))) (headline (:standard-properties [2119 2119 2130 2368 2368 0 (:title) nil nil nil nil 2132 2366 1 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 9) t] :title (#("Install" 0 7 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2130 2130 2130 2368 2368 0 nil section nil nil nil 2130 2368 nil # nil nil #33]) (paragraph (:standard-properties [2130 2130 2130 2367 2368 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #39)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #39] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #39))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #34]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #40)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #40] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #44)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("settings.py" 0 11 (:parent #48)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #40))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #42))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #44))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #35]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Install redis. Make sure you add the setting:\n" 0 46 (:parent #41))) (fixed-width (:standard-properties [2913 2913 nil nil 2931 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "appendonly yes")))) (headline (:standard-properties [2931 2931 2952 5782 5782 0 (:title) nil nil nil nil 2954 5780 1 # nil nil #27] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [2952 2952 2986 4250 4250 0 (:title) section nil nil nil 2988 4248 2 # nil nil #36] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #39))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2986 2986 2986 4250 4250 0 nil section nil nil nil 2986 4250 nil # nil nil #39]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #42]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #45]) #("Note: we moved to MariaDB" 0 25 (:parent #48))) #("\n" 0 1 (:parent #45))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #46))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("As root configure and run\n" 0 26 (:parent #47))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #42] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # 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nil nil #42] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #56))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("When you get errors like:\n" 0 26 (:parent #58))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("you may need to set\n" 0 20 (:parent #60))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #36] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #40))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #40]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("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 #46)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("webqtl" 0 6 (:parent #50))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("s" 0 1 (:parent #51))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #46)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("webqtl" 0 6 (:parent #53))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("plant" 0 5 (:parent #54))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #46))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Download one database from\n" 0 27 (:parent #47))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #43]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #48))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #43]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #49))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Check the md5sum.\n" 0 18 (:parent #50))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #51))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #53))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("and\n" 0 4 (:parent #55))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #57))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #59))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #60))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Note for the plant database you can rename it to db" 0 51 (:parent #61)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("webqtl" 0 6 (:parent #65))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("s" 0 1 (:parent #66))) #(", or\nchange the settings in etc/default" 0 39 (:parent #61)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("settings.py" 0 11 (:parent #68))) #("to match your path.\n" 0 20 (:parent #61)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #37]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #43))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #40] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #44))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #38]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("See " 0 4 (:parent #44)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #44))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #39]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #45)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #45))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #40] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #43))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #43]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #49)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PATH" 0 4 (:parent #53))) #("and R" 0 5 (:parent #49)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("LIBS" 0 4 (:parent #55))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("SITE" 0 4 (:parent #56))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #49))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("On one system:\n" 0 15 (:parent #51))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #46] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #46]) #("and perhaps a few more.\n" 0 24 (:parent #53))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #40] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #44)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("data" 0 4 (:parent #56))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #44)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("files" 0 5 (:parent #58))) #("/genotype'" 0 10 (:parent #44))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #44]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #50)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("data" 0 4 (:parent #54))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #50)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("settings.py" 0 11 (:parent #56))) #("(see above in\nthis document).\n" 0 30 (:parent #50))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("You can use the GENENETWORK" 0 27 (:parent #51)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("FILES" 0 5 (:parent #55))) #("switch to set the datadir, for example\n" 0 39 (:parent #51))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #40] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #45]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #48]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #51))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #40] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #46]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("This error\n" 0 11 (:parent #52))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #54))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #55)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("LIBS" 0 4 (:parent #59))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("SITE" 0 4 (:parent #60))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #55))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #40] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #47))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #47]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #50]) #("The following error\n" 0 20 (:parent #53))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("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 #55))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #57))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #59)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("URI" 0 3 (:parent #63))) #("to something like\n" 0 18 (:parent #59))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #50] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #41]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #47))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("#+begin" 0 7 (:parent #48)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("src" 0 3 (:parent #52))) #("\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 #48))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #49))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #44]) #(" yes\n env GUIX" 0 30 (:parent #50)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #54))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PATH" 0 4 (:parent #55))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #50))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("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 #51))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #44]) #(" 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 #52)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #56))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PATH" 0 4 (:parent #57))) #("=../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 #52))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("/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 #53))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #44]) #(" which should have the same HASH values " 0 48 (:parent #54)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #54]) #("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 #58))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #54)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #54] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #54)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #54] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #54)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #64))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("PATH" 0 4 (:parent #65))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #54)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #54] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #54)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #69))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("PATH" 0 4 (:parent #70))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #54)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #72))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("PATH" 0 4 (:parent #73))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #54)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #54] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #54))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #22))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #17)]) #12)] :type unordered) . #0)] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [538 538 538 564 564 0 nil nil nil nil nil nil nil nil # nil nil #7]) (link (:standard-properties [538 nil 552 561 563 0 nil nil nil nil nil nil nil nil # nil nil #10] :type "custom-id" :type-explicit-p nil :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil) #("Read more" 0 9 (:parent #13))) #("\n" 0 1 (:parent #10)))) (item (:standard-properties [564 564 567 1119 1119 0 (:tag) item nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) (plain-list (:standard-properties [121 121 121 1230 1231 1 nil planning nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) (section (:standard-properties [121 121 121 1231 1231 0 nil section nil nil nil 121 1231 nil # nil nil (headline (:standard-properties [43 43 121 1231 1231 0 (:title) nil nil nil nil 123 1229 1 # nil nil (org-data (:standard-properties [1 1 1 15256 15256 0 nil org-data nil nil nil 3 15256 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 43 43 0 nil first-section nil nil nil 1 43 nil # nil nil #28]) (keyword (:standard-properties [1 1 nil nil 43 1 nil top-comment nil nil nil nil nil nil # nil nil #31] :key "TITLE" :value "Installing GeneNetwork services"))) #23 (headline (:standard-properties [1231 1231 1247 2119 2119 0 (:title) nil nil nil nil 1249 2117 1 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1247 1247 1247 2119 2119 0 nil section nil nil nil 1247 2119 nil # nil nil #33]) (paragraph (:standard-properties [1247 1247 1247 1632 1633 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("Large system deployments can get very " 0 38 (:parent #39)) (link (:standard-properties [1285 nil 1337 1344 1346 0 nil nil nil nil nil nil nil nil # nil nil #39] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil) #("complex" 0 7 (:parent #43))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #39)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #39] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #45))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #39))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #40)) (link (:standard-properties [1851 nil 1905 1924 1927 1 nil nil nil nil nil nil nil nil # nil nil #40] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #44))) #("and " 0 4 (:parent #40)) (link (:standard-properties [1931 nil 1970 1978 1980 0 nil nil nil nil nil nil nil nil # nil nil #40] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #46))) #(".\n" 0 2 (:parent #40))) (paragraph (:standard-properties [1983 1983 1983 2118 2119 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #41)) (link (:standard-properties [2069 nil 2094 2114 2116 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #45))) #(".\n" 0 2 (:parent #41))))) (headline (:standard-properties [2119 2119 2130 2368 2368 0 (:title) nil nil nil nil 2132 2366 1 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 9) t] :title (#("Install" 0 7 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2130 2130 2130 2368 2368 0 nil section nil nil nil 2130 2368 nil # nil nil #34]) (paragraph (:standard-properties [2130 2130 2130 2367 2368 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #40)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #40] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #40))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #35]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #41)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #45)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("settings.py" 0 11 (:parent #49)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #41))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #43))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #45))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #36]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("Install redis. Make sure you add the setting:\n" 0 46 (:parent #42))) (fixed-width (:standard-properties [2913 2913 nil nil 2931 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "appendonly yes")))) (headline (:standard-properties [2931 2931 2952 5782 5782 0 (:title) nil nil nil nil 2954 5780 1 # nil nil #28] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [2952 2952 2986 4250 4250 0 (:title) section nil nil nil 2988 4248 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #40))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2986 2986 2986 4250 4250 0 nil section nil nil nil 2986 4250 nil # nil nil #40]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #43]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #46]) #("Note: we moved to MariaDB" 0 25 (:parent #49))) #("\n" 0 1 (:parent #46))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #47))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("As root configure and run\n" 0 26 (:parent #48))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #43] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # 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nil nil #43] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #57))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("When you get errors like:\n" 0 26 (:parent #59))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("you may need to set\n" 0 20 (:parent #61))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #41))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #41]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #47)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("webqtl" 0 6 (:parent #51))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("s" 0 1 (:parent #52))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #47)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("webqtl" 0 6 (:parent #54))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("plant" 0 5 (:parent #55))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #47))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Download one database from\n" 0 27 (:parent #48))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #44]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #49))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #44]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #50] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #50))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Check the md5sum.\n" 0 18 (:parent #51))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #52))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #54))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("and\n" 0 4 (:parent #56))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #58))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #60))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #61))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Note for the plant database you can rename it to db" 0 51 (:parent #62)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("webqtl" 0 6 (:parent #66))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("s" 0 1 (:parent #67))) #(", or\nchange the settings in etc/default" 0 39 (:parent #62)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("settings.py" 0 11 (:parent #69))) #("to match your path.\n" 0 20 (:parent #62)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #38]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #44))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #41] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #45))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #39]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("See " 0 4 (:parent #45)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #45))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #40]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #46)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #46))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #41] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #44))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #44]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #50)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PATH" 0 4 (:parent #54))) #("and R" 0 5 (:parent #50)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("LIBS" 0 4 (:parent #56))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("SITE" 0 4 (:parent #57))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #50))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("On one system:\n" 0 15 (:parent #52))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #47] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #47]) #("and perhaps a few more.\n" 0 24 (:parent #54))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #41] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #45)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("data" 0 4 (:parent #57))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #45)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("files" 0 5 (:parent #59))) #("/genotype'" 0 10 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #45]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #51)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("data" 0 4 (:parent #55))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #51)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("settings.py" 0 11 (:parent #57))) #("(see above in\nthis document).\n" 0 30 (:parent #51))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("You can use the GENENETWORK" 0 27 (:parent #52)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("FILES" 0 5 (:parent #56))) #("switch to set the datadir, for example\n" 0 39 (:parent #52))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #41] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #46]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #49]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #52))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #41] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #47))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #47]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #50]) #("This error\n" 0 11 (:parent #53))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("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 #55))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #56)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("LIBS" 0 4 (:parent #60))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("SITE" 0 4 (:parent #61))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #56))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #41] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #48))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #48]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #51]) #("The following error\n" 0 20 (:parent #54))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #56))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #58))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #60)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #60] :use-brackets-p nil) #("URI" 0 3 (:parent #64))) #("to something like\n" 0 18 (:parent #60))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #51] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #42]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #48))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("#+begin" 0 7 (:parent #49)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("src" 0 3 (:parent #53))) #("\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 #49))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #50))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #45]) #(" yes\n env GUIX" 0 30 (:parent #51)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #55))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PATH" 0 4 (:parent #56))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #51))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("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 #52))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #45]) #(" 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 #53)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #57))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PATH" 0 4 (:parent #58))) #("=../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 #53))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("/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 #54))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #45]) #(" which should have the same HASH values " 0 48 (:parent #55)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #55]) #("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 #59))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #55)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #55] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #55)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #55] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #55)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #65))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("PATH" 0 4 (:parent #66))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #55)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #55] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #55)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #70))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("PATH" 0 4 (:parent #71))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #55)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #73))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("PATH" 0 4 (:parent #74))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #55)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #55] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #55))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #23))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #18)]) #13)] :type unordered) . #0)] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [567 567 567 607 607 0 nil nil nil nil nil nil nil nil # 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #40)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #40] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #46))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #40))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #42))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #44))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #46))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #37]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("Install redis. 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nil nil #44]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #47)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #47))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #45]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #51)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PATH" 0 4 (:parent #55))) #("and R" 0 5 (:parent #51)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("LIBS" 0 4 (:parent #57))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("SITE" 0 4 (:parent #58))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #51))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("On one system:\n" 0 15 (:parent #53))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #48] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #48]) #("and perhaps a few more.\n" 0 24 (:parent #55))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #46)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("data" 0 4 (:parent #58))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #46)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("files" 0 5 (:parent #60))) #("/genotype'" 0 10 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #46]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #52)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("data" 0 4 (:parent #56))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #52)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("settings.py" 0 11 (:parent #58))) #("(see above in\nthis document).\n" 0 30 (:parent #52))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("You can use the GENENETWORK" 0 27 (:parent #53)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("FILES" 0 5 (:parent #57))) #("switch to set the datadir, for example\n" 0 39 (:parent #53))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #47))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #47]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #50]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #53))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #48))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #48]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #51]) #("This error\n" 0 11 (:parent #54))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #56))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #57)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("LIBS" 0 4 (:parent #61))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("SITE" 0 4 (:parent #62))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #57))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #49))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #49]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #52]) #("The following error\n" 0 20 (:parent #55))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #57))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #59))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #61)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("URI" 0 3 (:parent #65))) #("to something like\n" 0 18 (:parent #61))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #52] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #43]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #49))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("#+begin" 0 7 (:parent #50)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("src" 0 3 (:parent #54))) #("\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 #50))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #51))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #46]) #(" yes\n env GUIX" 0 30 (:parent #52)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #56))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PATH" 0 4 (:parent #57))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #52))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("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 #53))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #46]) #(" 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 #54)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #58))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("PATH" 0 4 (:parent #59))) #("=../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 #54))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("/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 #55))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #46]) #(" which should have the same HASH values " 0 48 (:parent #56)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #56]) #("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 #60))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #56)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #56] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #56)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #56] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #56)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #66))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("PATH" 0 4 (:parent #67))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #56)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #56] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #56)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #71))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("PATH" 0 4 (:parent #72))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #56)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #74))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("PATH" 0 4 (:parent #75))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #56)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #56] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #56))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #24))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #19)]) #14)] :type unordered) . #0)] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [1122 1122 1122 1152 1152 0 nil nil nil nil nil nil nil nil # nil nil #9]) (link (:standard-properties [1122 nil 1138 1149 1151 0 nil nil nil nil nil nil nil nil # nil nil #12] :type "custom-id" :type-explicit-p nil :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil) #("IRC session" 0 11 (:parent #15))) #("\n" 0 1 (:parent #12)))) (item (:standard-properties [1152 1152 1155 1230 1230 0 (:tag) item nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) (plain-list (:standard-properties [121 121 121 1230 1231 1 nil planning nil nil nil nil nil nil # 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nil nil #33] :key "TITLE" :value "Installing GeneNetwork services"))) #25 (headline (:standard-properties [1231 1231 1247 2119 2119 0 (:title) nil nil nil nil 1249 2117 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1247 1247 1247 2119 2119 0 nil section nil nil nil 1247 2119 nil # nil nil #35]) (paragraph (:standard-properties [1247 1247 1247 1632 1633 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Large system deployments can get very " 0 38 (:parent #41)) (link (:standard-properties [1285 nil 1337 1344 1346 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil) #("complex" 0 7 (:parent #45))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #41)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #47))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #41))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #42)) (link (:standard-properties [1851 nil 1905 1924 1927 1 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #46))) #("and " 0 4 (:parent #42)) (link (:standard-properties [1931 nil 1970 1978 1980 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #48))) #(".\n" 0 2 (:parent #42))) (paragraph (:standard-properties [1983 1983 1983 2118 2119 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #43)) (link (:standard-properties [2069 nil 2094 2114 2116 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #47))) #(".\n" 0 2 (:parent #43))))) (headline (:standard-properties [2119 2119 2130 2368 2368 0 (:title) nil nil nil nil 2132 2366 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 9) t] :title (#("Install" 0 7 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2130 2130 2130 2368 2368 0 nil section nil nil nil 2130 2368 nil # nil nil #36]) (paragraph (:standard-properties [2130 2130 2130 2367 2368 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #42)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #42] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #42))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #37]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #43)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #47)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("settings.py" 0 11 (:parent #51)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #43))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #45))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #47))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #38]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("Install redis. 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nil nil #42]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #45]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #48]) #("Note: we moved to MariaDB" 0 25 (:parent #51))) #("\n" 0 1 (:parent #48))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #49))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("As root configure and run\n" 0 26 (:parent #50))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #45] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # 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Currently we have two databases for deployment,\n'db" 0 163 (:parent #49)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("webqtl" 0 6 (:parent #53))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("s" 0 1 (:parent #54))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #49)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("webqtl" 0 6 (:parent #56))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("plant" 0 5 (:parent #57))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #49))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Download one database from\n" 0 27 (:parent #50))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #46]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #51))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #46]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #52))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Check the md5sum.\n" 0 18 (:parent #53))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #54))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #56))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("and\n" 0 4 (:parent #58))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #60))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #62))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #63))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Note for the plant database you can rename it to db" 0 51 (:parent #64)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #64] :use-brackets-p nil) #("webqtl" 0 6 (:parent #68))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #64] :use-brackets-p nil) #("s" 0 1 (:parent #69))) #(", or\nchange the settings in etc/default" 0 39 (:parent #64)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # 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nil nil #43] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #47))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #41]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("See " 0 4 (:parent #47)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #47))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #42]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #48)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #48))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #46]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #52)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PATH" 0 4 (:parent #56))) #("and R" 0 5 (:parent #52)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("LIBS" 0 4 (:parent #58))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("SITE" 0 4 (:parent #59))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #52))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("On one system:\n" 0 15 (:parent #54))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #49] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #49]) #("and perhaps a few more.\n" 0 24 (:parent #56))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #47)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("data" 0 4 (:parent #59))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #47)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("files" 0 5 (:parent #61))) #("/genotype'" 0 10 (:parent #47))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #47]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #50]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #53)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("data" 0 4 (:parent #57))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #53)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("settings.py" 0 11 (:parent #59))) #("(see above in\nthis document).\n" 0 30 (:parent #53))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("You can use the GENENETWORK" 0 27 (:parent #54)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("FILES" 0 5 (:parent #58))) #("switch to set the datadir, for example\n" 0 39 (:parent #54))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #48))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #48]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #51]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #54))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #49))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #49]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #52]) #("This error\n" 0 11 (:parent #55))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #57))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #58)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("LIBS" 0 4 (:parent #62))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("SITE" 0 4 (:parent #63))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #58))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #50))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #50]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #53]) #("The following error\n" 0 20 (:parent #56))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #58))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #60))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #62)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("URI" 0 3 (:parent #66))) #("to something like\n" 0 18 (:parent #62))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #53] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #44))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #44]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #50))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("#+begin" 0 7 (:parent #51)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("src" 0 3 (:parent #55))) #("\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 #51))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #52))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #47]) #(" yes\n env GUIX" 0 30 (:parent #53)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #57))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PATH" 0 4 (:parent #58))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #53))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("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 #54))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #47]) #(" 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 #55)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #59))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("PATH" 0 4 (:parent #60))) #("=../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 #55))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("/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 #56))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #47]) #(" which should have the same HASH values " 0 48 (:parent #57)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #57]) #("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 #61))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #57)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #57] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #57)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #57] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #57)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #67))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PATH" 0 4 (:parent #68))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #57)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #57] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #57)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #72))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PATH" 0 4 (:parent #73))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #57)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #75))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PATH" 0 4 (:parent #76))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #57)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #57] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #57))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #25))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #20)]) #15)] :type unordered) . #0)] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [1155 1155 1155 1173 1173 0 nil nil nil nil nil nil nil nil # 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nil nil #18] :key "TITLE" :value "Installing GeneNetwork services"))) #10 (headline (:standard-properties [1231 1231 1247 2119 2119 0 (:title) nil nil nil nil 1249 2117 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #20))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1247 1247 1247 2119 2119 0 nil section nil nil nil 1247 2119 nil # nil nil #20]) (paragraph (:standard-properties [1247 1247 1247 1632 1633 1 nil planning nil nil nil nil nil nil # nil nil #23]) #("Large system deployments can get very " 0 38 (:parent #26)) (link (:standard-properties [1285 nil 1337 1344 1346 0 nil nil nil nil nil nil nil nil # nil nil #26] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil) #("complex" 0 7 (:parent #30))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #26)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #26] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #32))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #26))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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Follow the instructions on\n" 0 117 (:parent #27)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #27] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. 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You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #28))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #30))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #32))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #23))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #23]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #26]) #("Install redis. 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Currently we have two databases for deployment,\n'db" 0 163 (:parent #34)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("webqtl" 0 6 (:parent #38))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("s" 0 1 (:parent #39))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #34)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("webqtl" 0 6 (:parent #41))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("plant" 0 5 (:parent #42))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #34))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("Download one database from\n" 0 27 (:parent #35))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #31]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #36] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #36))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #31]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #37))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("Check the md5sum.\n" 0 18 (:parent #38))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #39))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #31] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("restart MySQL service (mysqld). 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nil nil #30]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #33)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #33] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #33))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #28))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #31))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #31]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #37)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("PATH" 0 4 (:parent #41))) #("and R" 0 5 (:parent #37)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("LIBS" 0 4 (:parent #43))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("SITE" 0 4 (:parent #44))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #37))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("On one system:\n" 0 15 (:parent #39))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #34] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #34]) #("and perhaps a few more.\n" 0 24 (:parent #41))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #32)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("data" 0 4 (:parent #44))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #32)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("files" 0 5 (:parent #46))) #("/genotype'" 0 10 (:parent #32))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #32]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #38)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("data" 0 4 (:parent #42))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #38)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("settings.py" 0 11 (:parent #44))) #("(see above in\nthis document).\n" 0 30 (:parent #38))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("You can use the GENENETWORK" 0 27 (:parent #39)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("FILES" 0 5 (:parent #43))) #("switch to set the datadir, for example\n" 0 39 (:parent #39))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #33))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #33]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #36]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #39))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #34))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #34]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("This error\n" 0 11 (:parent #40))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("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 #42))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #43)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("LIBS" 0 4 (:parent #47))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("SITE" 0 4 (:parent #48))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #43))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #35))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #35]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("The following error\n" 0 20 (:parent #41))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #43))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #45))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #47)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("URI" 0 3 (:parent #51))) #("to something like\n" 0 18 (:parent #47))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #38] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #29))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #29]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #32]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #35))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("#+begin" 0 7 (:parent #36)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #36] :use-brackets-p nil) #("src" 0 3 (:parent #40))) #("\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 #36))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #37))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #32]) #(" yes\n env GUIX" 0 30 (:parent #38)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #42))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("PATH" 0 4 (:parent #43))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #38))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("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 #39))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #32]) #(" 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 #40)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #44))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("PATH" 0 4 (:parent #45))) #("=../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 #40))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("/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 #41))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #32]) #(" which should have the same HASH values " 0 48 (:parent #42)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #46))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #42)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #42)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #42] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #42)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #52))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("PATH" 0 4 (:parent #53))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #42)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #42)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #57))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("PATH" 0 4 (:parent #58))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #42)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #60))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("PATH" 0 4 (:parent #61))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #42)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #42))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #10))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #5)]) #0)] :type unordered) (item (:standard-properties [121 121 124 156 156 0 (:tag) item nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) #0] :bullet "- " 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You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #357))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #359))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #361))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #352))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #352]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #355]) #("Install redis. 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nil nil #356]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #359]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #362]) #("Note: we moved to MariaDB" 0 25 (:parent #365))) #("\n" 0 1 (:parent #362))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #363))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("As root configure and run\n" 0 26 (:parent #364))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #359] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("If you want to run as root you may have to set\n" 0 47 (:parent #366))) (fixed-width (:standard-properties [3523 3523 nil nil 3563 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [3563 3563 3563 3584 3585 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("You also need to set\n" 0 21 (:parent #368))) (fixed-width (:standard-properties [3585 3585 nil nil 3608 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [3608 3608 3608 3687 3688 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #370))) (paragraph (:standard-properties [3688 3688 3688 3756 3757 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #371))) (fixed-width (:standard-properties [3757 3757 nil nil 3872 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #373))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("When you get errors like:\n" 0 26 (:parent #375))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("you may need to set\n" 0 20 (:parent #377))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #353] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #357))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #357]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #360]) #("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 #363)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("webqtl" 0 6 (:parent #367))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("s" 0 1 (:parent #368))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #363)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("webqtl" 0 6 (:parent #370))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("plant" 0 5 (:parent #371))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #363))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Download one database from\n" 0 27 (:parent #364))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #360]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #365] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #365))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #360]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #366))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Check the md5sum.\n" 0 18 (:parent #367))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #368))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #370))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("and\n" 0 4 (:parent #372))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #374))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #376))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("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 #377))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Note for the plant database you can rename it to db" 0 51 (:parent #378)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("webqtl" 0 6 (:parent #382))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("s" 0 1 (:parent #383))) #(", or\nchange the settings in etc/default" 0 39 (:parent #378)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("settings.py" 0 11 (:parent #385))) #("to match your path.\n" 0 20 (:parent #378)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #354))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #354]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #357]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #360))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #357] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #361] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #361))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #355))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #355]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("See " 0 4 (:parent #361)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #361] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #361))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #356))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #356]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #359]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #362)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #362] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #362))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #357))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #360))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #360]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #363]) #("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 #366)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("PATH" 0 4 (:parent #370))) #("and R" 0 5 (:parent #366)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("LIBS" 0 4 (:parent #372))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("SITE" 0 4 (:parent #373))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #366))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #363] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #363]) #("On one system:\n" 0 15 (:parent #368))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #363] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #363]) #("and perhaps a few more.\n" 0 24 (:parent #370))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #361)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #361] :use-brackets-p nil) #("data" 0 4 (:parent #373))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #361)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #361] :use-brackets-p nil) #("files" 0 5 (:parent #375))) #("/genotype'" 0 10 (:parent #361))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #361]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #364]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #367)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("data" 0 4 (:parent #371))) #(". 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 #367)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("settings.py" 0 11 (:parent #373))) #("(see above in\nthis document).\n" 0 30 (:parent #367))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #364]) #("You can use the GENENETWORK" 0 27 (:parent #368)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #368] :use-brackets-p nil) #("FILES" 0 5 (:parent #372))) #("switch to set the datadir, for example\n" 0 39 (:parent #368))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #364] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #362))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #362]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #365]) #("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 #368))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #363))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #363]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #366]) #("This error\n" 0 11 (:parent #369))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #366] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #366]) #("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 #371))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #366]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #372)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("LIBS" 0 4 (:parent #376))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("SITE" 0 4 (:parent #377))) #(". 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 #372))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #364))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #364]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #367]) #("The following error\n" 0 20 (:parent #370))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("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 #372))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #374))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #376)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #376] :use-brackets-p nil) #("URI" 0 3 (:parent #380))) #("to something like\n" 0 18 (:parent #376))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #367] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #358))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #358]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #361]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #364))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("#+begin" 0 7 (:parent #365)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("src" 0 3 (:parent #369))) #("\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 #365))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #366))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #361]) #(" yes\n env GUIX" 0 30 (:parent #367)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #371))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("PATH" 0 4 (:parent #372))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #367))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("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 #368))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #361]) #(" 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 #369)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #369] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #373))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #369] :use-brackets-p nil) #("PATH" 0 4 (:parent #374))) #("=../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 #369))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("/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 #370))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #361]) #(" which should have the same HASH values " 0 48 (:parent #371)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #371]) #("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 #375))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #371)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #371)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #371)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #381))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #382))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #371)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #371)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #386))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #387))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #371)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #389))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #390))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #371)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #371)))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((plain-list (:standard-properties [121 121 121 1230 1231 1 nil planning nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) (section (:standard-properties [121 121 121 1231 1231 0 nil section nil nil nil 121 1231 nil # nil nil (headline (:standard-properties [43 43 121 1231 1231 0 (:title) nil nil nil nil 123 1229 1 # nil nil (org-data (:standard-properties [1 1 1 15256 15256 0 nil org-data nil nil nil 3 15256 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 43 43 0 nil first-section nil nil nil 1 43 nil # nil nil #15]) (keyword (:standard-properties [1 1 nil nil 43 1 nil top-comment nil nil nil nil nil nil # nil nil #18] :key "TITLE" :value "Installing GeneNetwork services"))) #10 (headline (:standard-properties [1231 1231 1247 2119 2119 0 (:title) nil nil nil nil 1249 2117 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #20))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1247 1247 1247 2119 2119 0 nil section nil nil nil 1247 2119 nil # nil nil #20]) (paragraph (:standard-properties [1247 1247 1247 1632 1633 1 nil planning nil nil nil nil nil nil # nil nil #23]) #("Large system deployments can get very " 0 38 (:parent #26)) (link (:standard-properties [1285 nil 1337 1344 1346 0 nil nil nil nil nil nil nil nil # nil nil #26] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil) #("complex" 0 7 (:parent #30))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #26)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #26] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #32))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #26))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #27)) (link (:standard-properties [1851 nil 1905 1924 1927 1 nil nil nil nil nil nil nil nil # nil nil #27] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #31))) #("and " 0 4 (:parent #27)) (link (:standard-properties [1931 nil 1970 1978 1980 0 nil nil nil nil nil nil nil nil # nil nil #27] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #33))) #(".\n" 0 2 (:parent #27))) (paragraph (:standard-properties [1983 1983 1983 2118 2119 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #28)) (link (:standard-properties [2069 nil 2094 2114 2116 0 nil nil nil nil nil nil nil nil # nil nil #28] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #32))) #(".\n" 0 2 (:parent #28))))) (headline (:standard-properties [2119 2119 2130 2368 2368 0 (:title) nil nil nil nil 2132 2366 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 9) t] :title (#("Install" 0 7 (:parent #21))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2130 2130 2130 2368 2368 0 nil section nil nil nil 2130 2368 nil # nil nil #21]) (paragraph (:standard-properties [2130 2130 2130 2367 2368 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #27)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #27] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #27))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #22))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #22]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #25]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #28)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #28] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #32)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("settings.py" 0 11 (:parent #36)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #28))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #30))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #32))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #23))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #23]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #26]) #("Install redis. Make sure you add the setting:\n" 0 46 (:parent #29))) (fixed-width (:standard-properties [2913 2913 nil nil 2931 2 nil nil nil nil nil nil nil nil # nil nil #26] :value "appendonly yes")))) (headline (:standard-properties [2931 2931 2952 5782 5782 0 (:title) nil nil nil nil 2954 5780 1 # nil nil #15] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #24))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [2952 2952 2986 4250 4250 0 (:title) section nil nil nil 2988 4248 2 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #27))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2986 2986 2986 4250 4250 0 nil section nil nil nil 2986 4250 nil # nil nil #27]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #30]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #33]) #("Note: we moved to MariaDB" 0 25 (:parent #36))) #("\n" 0 1 (:parent #33))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #34))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("As root configure and run\n" 0 26 (:parent #35))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #30] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("If you want to run as root you may have to set\n" 0 47 (:parent #37))) (fixed-width (:standard-properties [3523 3523 nil nil 3563 2 nil nil nil nil nil nil nil nil # nil nil #30] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [3563 3563 3563 3584 3585 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("You also need to set\n" 0 21 (:parent #39))) (fixed-width (:standard-properties [3585 3585 nil nil 3608 2 nil nil nil nil nil nil nil nil # nil nil #30] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [3608 3608 3608 3687 3688 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #41))) (paragraph (:standard-properties [3688 3688 3688 3756 3757 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #42))) (fixed-width (:standard-properties [3757 3757 nil nil 3872 2 nil nil nil nil nil nil nil nil # nil nil #30] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #44))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #30] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("When you get errors like:\n" 0 26 (:parent #46))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #30] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("you may need to set\n" 0 20 (:parent #48))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #30] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #28))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #28]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #31]) #("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 #34)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("webqtl" 0 6 (:parent #38))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("s" 0 1 (:parent #39))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #34)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("webqtl" 0 6 (:parent #41))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("plant" 0 5 (:parent #42))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #34))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("Download one database from\n" 0 27 (:parent #35))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #31]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #36] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #36))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #31]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #37))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("Check the md5sum.\n" 0 18 (:parent #38))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #39))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #31] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #41))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #31] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("and\n" 0 4 (:parent #43))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #31] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #45))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #31] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #47))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("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 #48))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("Note for the plant database you can rename it to db" 0 51 (:parent #49)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("webqtl" 0 6 (:parent #53))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("s" 0 1 (:parent #54))) #(", or\nchange the settings in etc/default" 0 39 (:parent #49)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # 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nil nil #28] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #32))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #26))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #26]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #29]) #("See " 0 4 (:parent #32)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #32))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #27))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #27]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #30]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #33)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #33] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #33))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #28))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #31))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #31]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #37)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("PATH" 0 4 (:parent #41))) #("and R" 0 5 (:parent #37)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("LIBS" 0 4 (:parent #43))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("SITE" 0 4 (:parent #44))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #37))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("On one system:\n" 0 15 (:parent #39))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #34] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #34]) #("and perhaps a few more.\n" 0 24 (:parent #41))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #32)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("data" 0 4 (:parent #44))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #32)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("files" 0 5 (:parent #46))) #("/genotype'" 0 10 (:parent #32))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #32]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #38)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("data" 0 4 (:parent #42))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #38)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("settings.py" 0 11 (:parent #44))) #("(see above in\nthis document).\n" 0 30 (:parent #38))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("You can use the GENENETWORK" 0 27 (:parent #39)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("FILES" 0 5 (:parent #43))) #("switch to set the datadir, for example\n" 0 39 (:parent #39))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #33))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #33]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #36]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #39))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #34))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #34]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("This error\n" 0 11 (:parent #40))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("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 #42))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #43)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("LIBS" 0 4 (:parent #47))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("SITE" 0 4 (:parent #48))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #43))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #35))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #35]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("The following error\n" 0 20 (:parent #41))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #43))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #45))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #47)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("URI" 0 3 (:parent #51))) #("to something like\n" 0 18 (:parent #47))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #38] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #29))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #29]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #32]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #35))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("#+begin" 0 7 (:parent #36)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #36] :use-brackets-p nil) #("src" 0 3 (:parent #40))) #("\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 #36))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #37))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #32]) #(" yes\n env GUIX" 0 30 (:parent #38)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #42))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("PATH" 0 4 (:parent #43))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #38))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("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 #39))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #32]) #(" 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 #40)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #44))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("PATH" 0 4 (:parent #45))) #("=../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 #40))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("/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 #41))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #32]) #(" which should have the same HASH values " 0 48 (:parent #42)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #46))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #42)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #42)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #42] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #42)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #52))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("PATH" 0 4 (:parent #53))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #42)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #42)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #57))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("PATH" 0 4 (:parent #58))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #42)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #60))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("PATH" 0 4 (:parent #61))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #42)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #42))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #10))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #5)]) #0)] :type unordered) (item (:standard-properties [121 121 124 156 156 0 (:tag) item nil nil nil nil nil nil # 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nil nil #31]) #("If you want to run as root you may have to set\n" 0 47 (:parent #38))) (fixed-width (:standard-properties [3523 3523 nil nil 3563 2 nil nil nil nil nil nil nil nil # nil nil #31] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [3563 3563 3563 3584 3585 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("You also need to set\n" 0 21 (:parent #40))) (fixed-width (:standard-properties [3585 3585 nil nil 3608 2 nil nil nil nil nil nil nil nil # nil nil #31] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [3608 3608 3608 3687 3688 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #42))) (paragraph (:standard-properties [3688 3688 3688 3756 3757 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #43))) (fixed-width (:standard-properties [3757 3757 nil nil 3872 2 nil nil nil nil nil nil nil nil # nil nil #31] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #45))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #31] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("When you get errors like:\n" 0 26 (:parent #47))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #31] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # 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Currently we have two databases for deployment,\n'db" 0 163 (:parent #35)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #35] :use-brackets-p nil) #("webqtl" 0 6 (:parent #39))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #35] :use-brackets-p nil) #("s" 0 1 (:parent #40))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #35)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #35] :use-brackets-p nil) #("webqtl" 0 6 (:parent #42))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #35] :use-brackets-p nil) #("plant" 0 5 (:parent #43))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #35))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("Download one database from\n" 0 27 (:parent #36))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #32]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #37))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #32]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #38))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("Check the md5sum.\n" 0 18 (:parent #39))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #40))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #32] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #42))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #32] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("and\n" 0 4 (:parent #44))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #32] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #46))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #32] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #48))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("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 #49))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("Note for the plant database you can rename it to db" 0 51 (:parent #50)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("webqtl" 0 6 (:parent #54))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("s" 0 1 (:parent #55))) #(", or\nchange the settings in etc/default" 0 39 (:parent #50)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # 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nil nil #29] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #33] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #33))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #27))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #27]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #30]) #("See " 0 4 (:parent #33)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #33] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #33))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #28))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #28]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #31]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #34)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #34] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #34))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #29))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #32))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #32]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("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 #38)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("PATH" 0 4 (:parent #42))) #("and R" 0 5 (:parent #38)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("LIBS" 0 4 (:parent #44))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("SITE" 0 4 (:parent #45))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #38))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("On one system:\n" 0 15 (:parent #40))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #35] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #35]) #("and perhaps a few more.\n" 0 24 (:parent #42))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #33)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("data" 0 4 (:parent #45))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #33)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("files" 0 5 (:parent #47))) #("/genotype'" 0 10 (:parent #33))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #33]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #39)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("data" 0 4 (:parent #43))) #(". 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 #39)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("settings.py" 0 11 (:parent #45))) #("(see above in\nthis document).\n" 0 30 (:parent #39))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("You can use the GENENETWORK" 0 27 (:parent #40)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("FILES" 0 5 (:parent #44))) #("switch to set the datadir, for example\n" 0 39 (:parent #40))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #36] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #34))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #34]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #37]) #("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 #40))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #35))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #35]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("This error\n" 0 11 (:parent #41))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("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 #43))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #44)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("LIBS" 0 4 (:parent #48))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("SITE" 0 4 (:parent #49))) #(". 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 #44))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #36))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #36]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("The following error\n" 0 20 (:parent #42))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("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 #44))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #46))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #48)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("URI" 0 3 (:parent #52))) #("to something like\n" 0 18 (:parent #48))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #39] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #30))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #30]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #36))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("#+begin" 0 7 (:parent #37)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("src" 0 3 (:parent #41))) #("\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 #37))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #38))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #33]) #(" yes\n env GUIX" 0 30 (:parent #39)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #43))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("PATH" 0 4 (:parent #44))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #39))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("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 #40))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #33]) #(" 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 #41)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #45))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("PATH" 0 4 (:parent #46))) #("=../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 #41))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("/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 #42))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #33]) #(" which should have the same HASH values " 0 48 (:parent #43)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #43]) #("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 #47))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #43)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #43)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #43] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #43)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #53))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("PATH" 0 4 (:parent #54))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #43)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #43)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #58))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("PATH" 0 4 (:parent #59))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #43)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #61))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("PATH" 0 4 (:parent #62))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #43)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #43))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #11))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #6)]) . #0)] :type unordered) (item (:standard-properties [121 121 124 156 156 0 (:tag) item nil nil nil nil nil nil # 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nil nil #25]) #("If you want to run as root you may have to set\n" 0 47 (:parent #32))) (fixed-width (:standard-properties [3523 3523 nil nil 3563 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [3563 3563 3563 3584 3585 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("You also need to set\n" 0 21 (:parent #34))) (fixed-width (:standard-properties [3585 3585 nil nil 3608 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [3608 3608 3608 3687 3688 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #36))) (paragraph (:standard-properties [3688 3688 3688 3756 3757 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #37))) (fixed-width (:standard-properties [3757 3757 nil nil 3872 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #39))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("When you get errors like:\n" 0 26 (:parent #41))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("you may need to set\n" 0 20 (:parent #43))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #19] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #23))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #23]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #26]) #("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 #29)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #29] :use-brackets-p nil) #("webqtl" 0 6 (:parent #33))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #29] :use-brackets-p nil) #("s" 0 1 (:parent #34))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #29)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #29] :use-brackets-p nil) #("webqtl" 0 6 (:parent #36))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #29] :use-brackets-p nil) #("plant" 0 5 (:parent #37))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #29))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("Download one database from\n" 0 27 (:parent #30))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #26]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #31] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #31))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #26]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #32))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("Check the md5sum.\n" 0 18 (:parent #33))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #34))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #26] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #36))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #26] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("and\n" 0 4 (:parent #38))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #26] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #40))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #26] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #42))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("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 #43))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("Note for the plant database you can rename it to db" 0 51 (:parent #44)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("webqtl" 0 6 (:parent #48))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("s" 0 1 (:parent #49))) #(", or\nchange the settings in etc/default" 0 39 (:parent #44)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("settings.py" 0 11 (:parent #51))) #("to match your path.\n" 0 20 (:parent #44)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #20))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #20]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #23]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #26))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #23] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #27] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #27))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #21))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #21]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("See " 0 4 (:parent #27)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #27] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #27))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #22))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #22]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #25]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #28)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #28] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #28))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #23))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #26))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #26]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #29]) #("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 #32)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("PATH" 0 4 (:parent #36))) #("and R" 0 5 (:parent #32)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("LIBS" 0 4 (:parent #38))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("SITE" 0 4 (:parent #39))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #32))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #29] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("On one system:\n" 0 15 (:parent #34))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #29] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #29]) #("and perhaps a few more.\n" 0 24 (:parent #36))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #27)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("data" 0 4 (:parent #39))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #27)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("files" 0 5 (:parent #41))) #("/genotype'" 0 10 (:parent #27))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #27]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #30]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #33)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("data" 0 4 (:parent #37))) #(". 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 #33)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("settings.py" 0 11 (:parent #39))) #("(see above in\nthis document).\n" 0 30 (:parent #33))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("You can use the GENENETWORK" 0 27 (:parent #34)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("FILES" 0 5 (:parent #38))) #("switch to set the datadir, for example\n" 0 39 (:parent #34))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #30] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #28))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #28]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #31]) #("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 #34))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #29))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #29]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #32]) #("This error\n" 0 11 (:parent #35))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #32] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("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 #37))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #38)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("LIBS" 0 4 (:parent #42))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("SITE" 0 4 (:parent #43))) #(". 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 #38))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #30))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #30]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("The following error\n" 0 20 (:parent #36))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("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 #38))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #40))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #42)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("URI" 0 3 (:parent #46))) #("to something like\n" 0 18 (:parent #42))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #33] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #24))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #24]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #27]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #30))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("#+begin" 0 7 (:parent #31)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #31] :use-brackets-p nil) #("src" 0 3 (:parent #35))) #("\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 #31))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #32))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #27]) #(" yes\n env GUIX" 0 30 (:parent #33)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #37))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("PATH" 0 4 (:parent #38))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #33))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("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 #34))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #27]) #(" 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 #35)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #35] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #39))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #35] :use-brackets-p nil) #("PATH" 0 4 (:parent #40))) #("=../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 #35))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("/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 #36))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #27]) #(" which should have the same HASH values " 0 48 (:parent #37)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #37]) #("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 #41))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #37)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #37)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #37] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #37)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #47))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("PATH" 0 4 (:parent #48))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #37)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #37)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #52))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("PATH" 0 4 (:parent #53))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #37)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #55))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("PATH" 0 4 (:parent #56))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #37)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #37))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #5))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #0)]) (plain-list (:standard-properties [121 121 121 1230 1231 1 nil planning nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) #0] :type unordered) (item 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"xhtml-strict" :html-container "div" :html-content-class "content" :description nil :keywords nil :html-html5-fancy nil :html-link-use-abs-url nil :html-link-home "" :html-link-up "" :html-mathjax "" :html-equation-reference-format "\\eqref{%s}" :html-postamble auto :html-preamble t :html-head "" :html-head-extra "" :subtitle nil :html-head-include-default-style t :html-head-include-scripts nil :html-allow-name-attribute-in-anchors nil :html-divs ((preamble "div" "preamble") (content "div" "content") (postamble "div" "postamble")) :html-checkbox-type ascii :html-extension "html" :html-footnote-format "%s" :html-footnote-separator ", " :html-footnotes-section "
\n

%s:

\n
\n%s\n
\n
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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #355)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #355] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #361))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #355))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #352]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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Follow the instructions on\n" 0 117 (:parent #356)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #356] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. 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You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #357))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #359))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #361))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #352))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #352]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #355]) #("Install redis. 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Currently we have two databases for deployment,\n'db" 0 163 (:parent #363)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("webqtl" 0 6 (:parent #367))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("s" 0 1 (:parent #368))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #363)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("webqtl" 0 6 (:parent #370))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("plant" 0 5 (:parent #371))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #363))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Download one database from\n" 0 27 (:parent #364))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #360]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #365] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #365))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #360]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #366))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Check the md5sum.\n" 0 18 (:parent #367))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #368))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #370))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("and\n" 0 4 (:parent #372))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #374))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #376))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("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 #377))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Note for the plant database you can rename it to db" 0 51 (:parent #378)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("webqtl" 0 6 (:parent #382))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("s" 0 1 (:parent #383))) #(", or\nchange the settings in etc/default" 0 39 (:parent #378)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("settings.py" 0 11 (:parent #385))) #("to match your path.\n" 0 20 (:parent #378)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #354))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #354]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #357]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #360))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #357] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #361] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #361))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #355))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #355]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("See " 0 4 (:parent #361)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #361] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #361))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #356))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #356]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #359]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #362)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #362] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #362))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #357))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #360))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #360]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #363]) #("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 #366)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("PATH" 0 4 (:parent #370))) #("and R" 0 5 (:parent #366)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("LIBS" 0 4 (:parent #372))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("SITE" 0 4 (:parent #373))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #366))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #363] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #363]) #("On one system:\n" 0 15 (:parent #368))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #363] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #363]) #("and perhaps a few more.\n" 0 24 (:parent #370))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #361)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #361] :use-brackets-p nil) #("data" 0 4 (:parent #373))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #361)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #361] :use-brackets-p nil) #("files" 0 5 (:parent #375))) #("/genotype'" 0 10 (:parent #361))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #361]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #364]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #367)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("data" 0 4 (:parent #371))) #(". 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 #367)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("settings.py" 0 11 (:parent #373))) #("(see above in\nthis document).\n" 0 30 (:parent #367))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #364]) #("You can use the GENENETWORK" 0 27 (:parent #368)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #368] :use-brackets-p nil) #("FILES" 0 5 (:parent #372))) #("switch to set the datadir, for example\n" 0 39 (:parent #368))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #364] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #362))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #362]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #365]) #("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 #368))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #363))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #363]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #366]) #("This error\n" 0 11 (:parent #369))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #366] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #366]) #("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 #371))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #366]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #372)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("LIBS" 0 4 (:parent #376))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("SITE" 0 4 (:parent #377))) #(". 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 #372))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #364))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #364]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #367]) #("The following error\n" 0 20 (:parent #370))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("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 #372))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #374))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #376)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #376] :use-brackets-p nil) #("URI" 0 3 (:parent #380))) #("to something like\n" 0 18 (:parent #376))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #367] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #358))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #358]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #361]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #364))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("#+begin" 0 7 (:parent #365)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("src" 0 3 (:parent #369))) #("\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 #365))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #366))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #361]) #(" yes\n env GUIX" 0 30 (:parent #367)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #371))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("PATH" 0 4 (:parent #372))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #367))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("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 #368))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #361]) #(" 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 #369)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #369] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #373))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #369] :use-brackets-p nil) #("PATH" 0 4 (:parent #374))) #("=../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 #369))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("/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 #370))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #361]) #(" which should have the same HASH values " 0 48 (:parent #371)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #371]) #("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 #375))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #371)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #371)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #371)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #381))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #382))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #371)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #371)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #386))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #387))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #371)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #389))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #390))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #371)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #371)))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((section (:standard-properties [121 121 121 1231 1231 0 nil section nil nil nil 121 1231 nil # nil nil (headline (:standard-properties [43 43 121 1231 1231 0 (:title) nil nil nil nil 123 1229 1 # nil nil (org-data (:standard-properties [1 1 1 15256 15256 0 nil org-data nil nil nil 3 15256 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 43 43 0 nil first-section nil nil nil 1 43 nil # nil nil #10]) (keyword (:standard-properties [1 1 nil nil 43 1 nil top-comment nil nil nil nil nil nil # nil nil #13] :key "TITLE" :value "Installing GeneNetwork services"))) #5 (headline (:standard-properties [1231 1231 1247 2119 2119 0 (:title) nil nil nil nil 1249 2117 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #15))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1247 1247 1247 2119 2119 0 nil section nil nil nil 1247 2119 nil # nil nil #15]) (paragraph (:standard-properties [1247 1247 1247 1632 1633 1 nil planning nil nil nil nil nil nil # nil nil #18]) #("Large system deployments can get very " 0 38 (:parent #21)) (link (:standard-properties [1285 nil 1337 1344 1346 0 nil nil nil nil nil nil nil nil # nil nil #21] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil) #("complex" 0 7 (:parent #25))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #21)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #21] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #27))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #21))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("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 #22)) (link (:standard-properties [1851 nil 1905 1924 1927 1 nil nil nil nil nil nil nil nil # nil nil #22] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #26))) #("and " 0 4 (:parent #22)) (link (:standard-properties [1931 nil 1970 1978 1980 0 nil nil nil nil nil nil nil nil # nil nil #22] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #28))) #(".\n" 0 2 (:parent #22))) (paragraph (:standard-properties [1983 1983 1983 2118 2119 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #23)) (link (:standard-properties [2069 nil 2094 2114 2116 0 nil nil nil nil nil nil nil nil # nil nil #23] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #27))) #(".\n" 0 2 (:parent #23))))) (headline (:standard-properties [2119 2119 2130 2368 2368 0 (:title) nil nil nil nil 2132 2366 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 9) t] :title (#("Install" 0 7 (:parent #16))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2130 2130 2130 2368 2368 0 nil section nil nil nil 2130 2368 nil # nil nil #16]) (paragraph (:standard-properties [2130 2130 2130 2367 2368 1 nil planning nil nil nil nil nil nil # nil nil #19]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #22)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #22] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #22))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #17))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #17]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #20]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #23)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #23] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #27)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("settings.py" 0 11 (:parent #31)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #23))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #20] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #25))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #20] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #27))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #18))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #18]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #21]) #("Install redis. Make sure you add the setting:\n" 0 46 (:parent #24))) (fixed-width (:standard-properties [2913 2913 nil nil 2931 2 nil nil nil nil nil nil nil nil # nil nil #21] :value "appendonly yes")))) (headline (:standard-properties [2931 2931 2952 5782 5782 0 (:title) nil nil nil nil 2954 5780 1 # nil nil #10] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #19))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [2952 2952 2986 4250 4250 0 (:title) section nil nil nil 2988 4248 2 # nil nil #19] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #22))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2986 2986 2986 4250 4250 0 nil section nil nil nil 2986 4250 nil # nil nil #22]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #25]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #28]) #("Note: we moved to MariaDB" 0 25 (:parent #31))) #("\n" 0 1 (:parent #28))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #29))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("As root configure and run\n" 0 26 (:parent #30))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #25] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("If you want to run as root you may have to set\n" 0 47 (:parent #32))) (fixed-width (:standard-properties [3523 3523 nil nil 3563 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [3563 3563 3563 3584 3585 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("You also need to set\n" 0 21 (:parent #34))) (fixed-width (:standard-properties [3585 3585 nil nil 3608 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [3608 3608 3608 3687 3688 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #36))) (paragraph (:standard-properties [3688 3688 3688 3756 3757 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #37))) (fixed-width (:standard-properties [3757 3757 nil nil 3872 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #39))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("When you get errors like:\n" 0 26 (:parent #41))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("you may need to set\n" 0 20 (:parent #43))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #19] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #23))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #23]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #26]) #("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 #29)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #29] :use-brackets-p nil) #("webqtl" 0 6 (:parent #33))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #29] :use-brackets-p nil) #("s" 0 1 (:parent #34))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #29)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #29] :use-brackets-p nil) #("webqtl" 0 6 (:parent #36))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #29] :use-brackets-p nil) #("plant" 0 5 (:parent #37))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #29))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("Download one database from\n" 0 27 (:parent #30))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #26]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #31] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #31))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #26]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #32))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("Check the md5sum.\n" 0 18 (:parent #33))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #34))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #26] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #36))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #26] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("and\n" 0 4 (:parent #38))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #26] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #40))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #26] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #42))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("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 #43))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("Note for the plant database you can rename it to db" 0 51 (:parent #44)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("webqtl" 0 6 (:parent #48))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("s" 0 1 (:parent #49))) #(", or\nchange the settings in etc/default" 0 39 (:parent #44)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("settings.py" 0 11 (:parent #51))) #("to match your path.\n" 0 20 (:parent #44)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #20))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #20]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #23]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #26))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #23] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #27] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #27))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #21))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #21]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("See " 0 4 (:parent #27)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #27] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #27))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #22))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #22]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #25]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #28)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #28] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #28))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #23))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #26))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #26]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #29]) #("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 #32)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("PATH" 0 4 (:parent #36))) #("and R" 0 5 (:parent #32)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("LIBS" 0 4 (:parent #38))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("SITE" 0 4 (:parent #39))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #32))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #29] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("On one system:\n" 0 15 (:parent #34))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #29] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #29]) #("and perhaps a few more.\n" 0 24 (:parent #36))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #27)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("data" 0 4 (:parent #39))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #27)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("files" 0 5 (:parent #41))) #("/genotype'" 0 10 (:parent #27))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #27]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #30]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #33)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("data" 0 4 (:parent #37))) #(". 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 #33)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("settings.py" 0 11 (:parent #39))) #("(see above in\nthis document).\n" 0 30 (:parent #33))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("You can use the GENENETWORK" 0 27 (:parent #34)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("FILES" 0 5 (:parent #38))) #("switch to set the datadir, for example\n" 0 39 (:parent #34))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #30] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #28))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #28]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #31]) #("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 #34))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #29))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #29]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #32]) #("This error\n" 0 11 (:parent #35))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #32] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("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 #37))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #38)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("LIBS" 0 4 (:parent #42))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("SITE" 0 4 (:parent #43))) #(". 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 #38))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #30))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #30]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("The following error\n" 0 20 (:parent #36))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("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 #38))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #40))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #42)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("URI" 0 3 (:parent #46))) #("to something like\n" 0 18 (:parent #42))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #33] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #24))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #24]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #27]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #30))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("#+begin" 0 7 (:parent #31)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #31] :use-brackets-p nil) #("src" 0 3 (:parent #35))) #("\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 #31))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #32))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #27]) #(" yes\n env GUIX" 0 30 (:parent #33)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #37))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("PATH" 0 4 (:parent #38))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #33))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("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 #34))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #27]) #(" 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 #35)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #35] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #39))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #35] :use-brackets-p nil) #("PATH" 0 4 (:parent #40))) #("=../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 #35))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("/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 #36))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #27]) #(" which should have the same HASH values " 0 48 (:parent #37)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #37]) #("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 #41))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #37)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #37)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #37] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #37)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #47))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("PATH" 0 4 (:parent #48))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #37)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #37)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #52))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("PATH" 0 4 (:parent #53))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #37)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #22)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #22] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #28))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #22))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #19]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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nil nil #27]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #43))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("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 #44))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("Note for the plant database you can rename it to db" 0 51 (:parent #45)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("webqtl" 0 6 (:parent #49))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("s" 0 1 (:parent #50))) #(", or\nchange the settings in etc/default" 0 39 (:parent #45)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("settings.py" 0 11 (:parent #52))) #("to match your path.\n" 0 20 (:parent #45)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #21))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #21]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #27))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #24] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #28] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #28))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #22))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #22]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #25]) #("See " 0 4 (:parent #28)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #28] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #28))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #23))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #23]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #26]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #29)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #29] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #29))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #24))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #27))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #27]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #30]) #("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 #33)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("PATH" 0 4 (:parent #37))) #("and R" 0 5 (:parent #33)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("LIBS" 0 4 (:parent #39))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("SITE" 0 4 (:parent #40))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #33))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #30] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("On one system:\n" 0 15 (:parent #35))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #30] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #30]) #("and perhaps a few more.\n" 0 24 (:parent #37))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #28)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #28] :use-brackets-p nil) #("data" 0 4 (:parent #40))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #28)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #28] :use-brackets-p nil) #("files" 0 5 (:parent #42))) #("/genotype'" 0 10 (:parent #28))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #28]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #31]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #34)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("data" 0 4 (:parent #38))) #(". 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 #34)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("settings.py" 0 11 (:parent #40))) #("(see above in\nthis document).\n" 0 30 (:parent #34))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("You can use the GENENETWORK" 0 27 (:parent #35)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #35] :use-brackets-p nil) #("FILES" 0 5 (:parent #39))) #("switch to set the datadir, for example\n" 0 39 (:parent #35))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #31] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #29))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #29]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #32]) #("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 #35))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #30))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #30]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("This error\n" 0 11 (:parent #36))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("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 #38))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #39)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("LIBS" 0 4 (:parent #43))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("SITE" 0 4 (:parent #44))) #(". 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 #39))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #31))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #31]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("The following error\n" 0 20 (:parent #37))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("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 #39))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #41))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #43)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("URI" 0 3 (:parent #47))) #("to something like\n" 0 18 (:parent #43))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #34] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #25))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #25]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #28]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #31))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("#+begin" 0 7 (:parent #32)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("src" 0 3 (:parent #36))) #("\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 #32))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #33))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #28]) #(" yes\n env GUIX" 0 30 (:parent #34)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #38))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("PATH" 0 4 (:parent #39))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #34))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("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 #35))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #28]) #(" 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 #36)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #36] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #40))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #36] :use-brackets-p nil) #("PATH" 0 4 (:parent #41))) #("=../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 #36))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("/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 #37))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #28]) #(" which should have the same HASH values " 0 48 (:parent #38)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #38]) #("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 #42))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #38)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #38)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #38] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #38)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #48))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("PATH" 0 4 (:parent #49))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #38)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #38)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #53))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("PATH" 0 4 (:parent #54))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #38)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #16)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #16] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #22))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #16))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #13]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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nil nil #21]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #37))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("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 #38))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("Note for the plant database you can rename it to db" 0 51 (:parent #39)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("webqtl" 0 6 (:parent #43))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("s" 0 1 (:parent #44))) #(", or\nchange the settings in etc/default" 0 39 (:parent #39)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("settings.py" 0 11 (:parent #46))) #("to match your path.\n" 0 20 (:parent #39)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #15))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #15]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #18]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #21))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #18] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #22] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #22))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #16))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #16]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #19]) #("See " 0 4 (:parent #22)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #22] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #22))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #17))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #17]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #20]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #23)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #23] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #23))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #18))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #18] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #21))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #21]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("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 #27)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("PATH" 0 4 (:parent #31))) #("and R" 0 5 (:parent #27)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("LIBS" 0 4 (:parent #33))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("SITE" 0 4 (:parent #34))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #27))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #24] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("On one system:\n" 0 15 (:parent #29))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #24] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #24]) #("and perhaps a few more.\n" 0 24 (:parent #31))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #18] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #22)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #22] :use-brackets-p nil) #("data" 0 4 (:parent #34))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #22)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #22] :use-brackets-p nil) #("files" 0 5 (:parent #36))) #("/genotype'" 0 10 (:parent #22))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #22]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #25]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #28)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #28] :use-brackets-p nil) #("data" 0 4 (:parent #32))) #(". 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 #28)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #28] :use-brackets-p nil) #("settings.py" 0 11 (:parent #34))) #("(see above in\nthis document).\n" 0 30 (:parent #28))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("You can use the GENENETWORK" 0 27 (:parent #29)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #29] :use-brackets-p nil) #("FILES" 0 5 (:parent #33))) #("switch to set the datadir, for example\n" 0 39 (:parent #29))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #18] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #23))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #23]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #26]) #("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 #29))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #18] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #24))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #24]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #27]) #("This error\n" 0 11 (:parent #30))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #27] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("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 #32))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #33)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("LIBS" 0 4 (:parent #37))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("SITE" 0 4 (:parent #38))) #(". 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 #33))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #18] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #25))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #25]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #28]) #("The following error\n" 0 20 (:parent #31))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("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 #33))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #35))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #37)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("URI" 0 3 (:parent #41))) #("to something like\n" 0 18 (:parent #37))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #28] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #19))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #19]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #22]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #25))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("#+begin" 0 7 (:parent #26)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #26] :use-brackets-p nil) #("src" 0 3 (:parent #30))) #("\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 #26))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #27))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #22]) #(" yes\n env GUIX" 0 30 (:parent #28)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #28] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #32))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #28] :use-brackets-p nil) #("PATH" 0 4 (:parent #33))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #28))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("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 #29))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #22]) #(" 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 #30)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #30] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #34))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #30] :use-brackets-p nil) #("PATH" 0 4 (:parent #35))) #("=../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 #30))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("/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 #31))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #22]) #(" which should have the same HASH values " 0 48 (:parent #32)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #32]) #("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 #36))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #32)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #32)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #32] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #32)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #42))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("PATH" 0 4 (:parent #43))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #32)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #32)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #47))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("PATH" 0 4 (:parent #48))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #32)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #50))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("PATH" 0 4 (:parent #51))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #32)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #32))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #0))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [121 121 121 1231 1231 0 nil section nil nil nil 121 1231 nil # nil nil #0]) (plain-list (:standard-properties [121 121 121 1230 1231 1 nil planning nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) #3] :type unordered) (item (:standard-properties [121 121 124 156 156 0 (:tag) item nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) #6] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [124 124 124 156 156 0 nil nil nil nil nil nil nil nil # nil nil #9]) (link (:standard-properties [124 nil 141 153 155 0 nil nil nil nil nil nil nil nil # nil nil #12] :type 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #355)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #355] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #361))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #355))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #352]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #356)) (link (:standard-properties [1851 nil 1905 1924 1927 1 nil nil nil nil nil nil nil nil # nil nil #356] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #360))) #("and " 0 4 (:parent #356)) (link (:standard-properties [1931 nil 1970 1978 1980 0 nil nil nil nil nil nil nil nil # nil nil #356] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #362))) #(".\n" 0 2 (:parent #356))) (paragraph (:standard-properties [1983 1983 1983 2118 2119 1 nil nil nil nil nil nil nil nil # nil nil #352]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #357)) (link (:standard-properties [2069 nil 2094 2114 2116 0 nil nil nil nil nil nil nil nil # nil nil #357] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #361))) #(".\n" 0 2 (:parent #357))))) (headline (:standard-properties [2119 2119 2130 2368 2368 0 (:title) nil nil nil nil 2132 2366 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 9) t] :title (#("Install" 0 7 (:parent #350))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2130 2130 2130 2368 2368 0 nil section nil nil nil 2130 2368 nil # nil nil #350]) (paragraph (:standard-properties [2130 2130 2130 2367 2368 1 nil planning nil nil nil nil nil nil # nil nil #353]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #356)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #356] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #356))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #351))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #351]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #354]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #357)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #357] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #361)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #361] :use-brackets-p nil) #("settings.py" 0 11 (:parent #365)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #357))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #359))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #361))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #352))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #352]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #355]) #("Install redis. Make sure you add the setting:\n" 0 46 (:parent #358))) (fixed-width (:standard-properties [2913 2913 nil nil 2931 2 nil nil nil nil nil nil nil nil # nil nil #355] :value "appendonly yes")))) (headline (:standard-properties [2931 2931 2952 5782 5782 0 (:title) nil nil nil nil 2954 5780 1 # nil nil #344] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #353))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [2952 2952 2986 4250 4250 0 (:title) section nil nil nil 2988 4248 2 # nil nil #353] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #356))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2986 2986 2986 4250 4250 0 nil section nil nil nil 2986 4250 nil # nil nil #356]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #359]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #362]) #("Note: we moved to MariaDB" 0 25 (:parent #365))) #("\n" 0 1 (:parent #362))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #363))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("As root configure and run\n" 0 26 (:parent #364))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #359] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("If you want to run as root you may have to set\n" 0 47 (:parent #366))) (fixed-width (:standard-properties [3523 3523 nil nil 3563 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [3563 3563 3563 3584 3585 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("You also need to set\n" 0 21 (:parent #368))) (fixed-width (:standard-properties [3585 3585 nil nil 3608 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [3608 3608 3608 3687 3688 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #370))) (paragraph (:standard-properties [3688 3688 3688 3756 3757 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #371))) (fixed-width (:standard-properties [3757 3757 nil nil 3872 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #373))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("When you get errors like:\n" 0 26 (:parent #375))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("you may need to set\n" 0 20 (:parent #377))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #353] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #357))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #357]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #360]) #("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 #363)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("webqtl" 0 6 (:parent #367))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("s" 0 1 (:parent #368))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #363)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("webqtl" 0 6 (:parent #370))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("plant" 0 5 (:parent #371))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #363))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Download one database from\n" 0 27 (:parent #364))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #360]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #365] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #365))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #360]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #366))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Check the md5sum.\n" 0 18 (:parent #367))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #368))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #370))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("and\n" 0 4 (:parent #372))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #374))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #376))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("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 #377))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Note for the plant database you can rename it to db" 0 51 (:parent #378)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("webqtl" 0 6 (:parent #382))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("s" 0 1 (:parent #383))) #(", or\nchange the settings in etc/default" 0 39 (:parent #378)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("settings.py" 0 11 (:parent #385))) #("to match your path.\n" 0 20 (:parent #378)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #354))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #354]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #357]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #360))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #357] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #361] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #361))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #355))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #355]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # 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The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #362))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #357))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #360))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #360]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #363]) #("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 #366)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("PATH" 0 4 (:parent #370))) #("and R" 0 5 (:parent #366)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("LIBS" 0 4 (:parent #372))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("SITE" 0 4 (:parent #373))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #366))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #363] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #363]) #("On one system:\n" 0 15 (:parent #368))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #363] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #363]) #("and perhaps a few more.\n" 0 24 (:parent #370))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #361)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #361] :use-brackets-p nil) #("data" 0 4 (:parent #373))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #361)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #361] :use-brackets-p nil) #("files" 0 5 (:parent #375))) #("/genotype'" 0 10 (:parent #361))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #361]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #364]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #367)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("data" 0 4 (:parent #371))) #(". 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 #367)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("settings.py" 0 11 (:parent #373))) #("(see above in\nthis document).\n" 0 30 (:parent #367))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #364]) #("You can use the GENENETWORK" 0 27 (:parent #368)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #368] :use-brackets-p nil) #("FILES" 0 5 (:parent #372))) #("switch to set the datadir, for example\n" 0 39 (:parent #368))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #364] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #362))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #362]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #365]) #("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 #368))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #363))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #363]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #366]) #("This error\n" 0 11 (:parent #369))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #366] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #366]) #("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 #371))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #366]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #372)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("LIBS" 0 4 (:parent #376))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("SITE" 0 4 (:parent #377))) #(". 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 #372))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #364))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #364]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #367]) #("The following error\n" 0 20 (:parent #370))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("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 #372))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #374))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #376)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #376] :use-brackets-p nil) #("URI" 0 3 (:parent #380))) #("to something like\n" 0 18 (:parent #376))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #367] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #358))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #358]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #361]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #364))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("#+begin" 0 7 (:parent #365)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("src" 0 3 (:parent #369))) #("\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 #365))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #366))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #361]) #(" yes\n env GUIX" 0 30 (:parent #367)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #371))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("PATH" 0 4 (:parent #372))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #367))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("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 #368))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #361]) #(" 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 #369)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #369] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #373))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #369] :use-brackets-p nil) #("PATH" 0 4 (:parent #374))) #("=../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 #369))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("/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 #370))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #361]) #(" which should have the same HASH values " 0 48 (:parent #371)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #371]) #("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 #375))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #371)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #371)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #371)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #381))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #382))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #371)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #371)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #386))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #387))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #371)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #389))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #390))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #371)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #371)))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((headline (:standard-properties [43 43 121 1231 1231 0 (:title) nil nil nil nil 123 1229 1 # nil nil (org-data (:standard-properties [1 1 1 15256 15256 0 nil org-data nil nil nil 3 15256 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 43 43 0 nil first-section nil nil nil 1 43 nil # nil nil #5]) (keyword (:standard-properties [1 1 nil nil 43 1 nil top-comment nil nil nil nil nil nil # nil nil #8] :key "TITLE" :value "Installing GeneNetwork services"))) #0 (headline (:standard-properties [1231 1231 1247 2119 2119 0 (:title) nil nil nil nil 1249 2117 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #10))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1247 1247 1247 2119 2119 0 nil section nil nil nil 1247 2119 nil # nil nil #10]) (paragraph (:standard-properties [1247 1247 1247 1632 1633 1 nil planning nil nil nil nil nil nil # nil nil #13]) #("Large system deployments can get very " 0 38 (:parent #16)) (link (:standard-properties [1285 nil 1337 1344 1346 0 nil nil nil nil nil nil nil nil # nil nil #16] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil) #("complex" 0 7 (:parent #20))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #16)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #16] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #22))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #16))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #13]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #17)) (link (:standard-properties [1851 nil 1905 1924 1927 1 nil nil nil nil nil nil nil nil # nil nil #17] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #21))) #("and " 0 4 (:parent #17)) (link (:standard-properties [1931 nil 1970 1978 1980 0 nil nil nil nil nil nil nil nil # nil nil #17] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #23))) #(".\n" 0 2 (:parent #17))) (paragraph (:standard-properties [1983 1983 1983 2118 2119 1 nil nil nil nil nil nil nil nil # nil nil #13]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #18)) (link (:standard-properties [2069 nil 2094 2114 2116 0 nil nil nil nil nil nil nil nil # nil nil #18] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #22))) #(".\n" 0 2 (:parent #18))))) (headline (:standard-properties [2119 2119 2130 2368 2368 0 (:title) nil nil nil nil 2132 2366 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 9) t] :title (#("Install" 0 7 (:parent #11))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2130 2130 2130 2368 2368 0 nil section nil nil nil 2130 2368 nil # nil nil #11]) (paragraph (:standard-properties [2130 2130 2130 2367 2368 1 nil planning nil nil nil nil nil nil # nil nil #14]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #17)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #17] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #17))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #12))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #12]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #15]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #18)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #18] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #22)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #22] :use-brackets-p nil) #("settings.py" 0 11 (:parent #26)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #18))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #15] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #15]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #20))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #15] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #15]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #22))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #13))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #13]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #16]) #("Install redis. Make sure you add the setting:\n" 0 46 (:parent #19))) (fixed-width (:standard-properties [2913 2913 nil nil 2931 2 nil nil nil nil nil nil nil nil # nil nil #16] :value "appendonly yes")))) (headline (:standard-properties [2931 2931 2952 5782 5782 0 (:title) nil nil nil nil 2954 5780 1 # nil nil #5] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #14))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [2952 2952 2986 4250 4250 0 (:title) section nil nil nil 2988 4248 2 # nil nil #14] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #17))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2986 2986 2986 4250 4250 0 nil section nil nil nil 2986 4250 nil # nil nil #17]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #20]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #23]) #("Note: we moved to MariaDB" 0 25 (:parent #26))) #("\n" 0 1 (:parent #23))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #24))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("As root configure and run\n" 0 26 (:parent #25))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #20] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("If you want to run as root you may have to set\n" 0 47 (:parent #27))) (fixed-width (:standard-properties [3523 3523 nil nil 3563 2 nil nil nil nil nil nil nil nil # nil nil #20] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [3563 3563 3563 3584 3585 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("You also need to set\n" 0 21 (:parent #29))) (fixed-width (:standard-properties [3585 3585 nil nil 3608 2 nil nil nil nil nil nil nil nil # nil nil #20] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [3608 3608 3608 3687 3688 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #31))) (paragraph (:standard-properties [3688 3688 3688 3756 3757 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #32))) (fixed-width (:standard-properties [3757 3757 nil nil 3872 2 nil nil nil nil nil nil nil nil # nil nil #20] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #34))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #20] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("When you get errors like:\n" 0 26 (:parent #36))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #20] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("you may need to set\n" 0 20 (:parent #38))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #20] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #14] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #18))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #18]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #21]) #("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 #24)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #24] :use-brackets-p nil) #("webqtl" 0 6 (:parent #28))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #24] :use-brackets-p nil) #("s" 0 1 (:parent #29))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #24)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #24] :use-brackets-p nil) #("webqtl" 0 6 (:parent #31))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #24] :use-brackets-p nil) #("plant" 0 5 (:parent #32))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #24))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("Download one database from\n" 0 27 (:parent #25))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #21]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #26] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #26))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #21]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #27] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #27))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("Check the md5sum.\n" 0 18 (:parent #28))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #29))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #21] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #31))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #21] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("and\n" 0 4 (:parent #33))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #21] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #35))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #21] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #37))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("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 #38))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("Note for the plant database you can rename it to db" 0 51 (:parent #39)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("webqtl" 0 6 (:parent #43))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("s" 0 1 (:parent #44))) #(", or\nchange the settings in etc/default" 0 39 (:parent #39)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("settings.py" 0 11 (:parent #46))) #("to match your path.\n" 0 20 (:parent #39)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #15))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #15]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #18]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #21))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #18] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #22] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #22))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #16))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #16]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #19]) #("See " 0 4 (:parent #22)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #22] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #22))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #17))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #17]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #20]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #23)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #23] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #23))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #18))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #18] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #21))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #21]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("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 #27)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("PATH" 0 4 (:parent #31))) #("and R" 0 5 (:parent #27)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("LIBS" 0 4 (:parent #33))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("SITE" 0 4 (:parent #34))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #27))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #24] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("On one system:\n" 0 15 (:parent #29))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #24] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #24]) #("and perhaps a few more.\n" 0 24 (:parent #31))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #18] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #22)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #22] :use-brackets-p nil) #("data" 0 4 (:parent #34))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #22)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #22] :use-brackets-p nil) #("files" 0 5 (:parent #36))) #("/genotype'" 0 10 (:parent #22))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #22]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #25]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #28)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #28] :use-brackets-p nil) #("data" 0 4 (:parent #32))) #(". 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 #28)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #28] :use-brackets-p nil) #("settings.py" 0 11 (:parent #34))) #("(see above in\nthis document).\n" 0 30 (:parent #28))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("You can use the GENENETWORK" 0 27 (:parent #29)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #29] :use-brackets-p nil) #("FILES" 0 5 (:parent #33))) #("switch to set the datadir, for example\n" 0 39 (:parent #29))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #18] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #23))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #23]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #26]) #("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 #29))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #18] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #24))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #24]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #27]) #("This error\n" 0 11 (:parent #30))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #27] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("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 #32))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #33)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("LIBS" 0 4 (:parent #37))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("SITE" 0 4 (:parent #38))) #(". 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 #33))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #18] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #25))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #25]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #28]) #("The following error\n" 0 20 (:parent #31))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("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 #33))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #35))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #37)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("URI" 0 3 (:parent #41))) #("to something like\n" 0 18 (:parent #37))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #28] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #19))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #19]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #22]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #25))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("#+begin" 0 7 (:parent #26)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #26] :use-brackets-p nil) #("src" 0 3 (:parent #30))) #("\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 #26))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #27))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #22]) #(" yes\n env GUIX" 0 30 (:parent #28)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #28] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #32))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #28] :use-brackets-p nil) #("PATH" 0 4 (:parent #33))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #28))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("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 #29))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #22]) #(" 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 #30)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #30] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #34))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #30] :use-brackets-p nil) #("PATH" 0 4 (:parent #35))) #("=../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 #30))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("/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 #31))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #22]) #(" which should have the same HASH values " 0 48 (:parent #32)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #32]) #("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 #36))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #32)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #32)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #32] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #32)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #42))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("PATH" 0 4 (:parent #43))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #32)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #32)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #47))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("PATH" 0 4 (:parent #48))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #32)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #50))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("PATH" 0 4 (:parent #51))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #32)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #32))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #0))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [121 121 121 1231 1231 0 nil section nil nil nil 121 1231 nil # nil nil #0]) (plain-list (:standard-properties [121 121 121 1230 1231 1 nil planning nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) #3] :type unordered) (item (:standard-properties [121 121 124 156 156 0 (:tag) item nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) #6] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [124 124 124 156 156 0 nil nil nil nil nil nil nil nil # 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #9)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #9] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #15))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #9))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #6]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #11))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #8] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #8]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #13))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #8] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #8]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #15))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil (org-data (:standard-properties [1 1 1 15256 15256 0 nil org-data nil nil nil 3 15256 nil # nil nil nil] :path nil :CATEGORY nil) . #0)] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #6))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #6]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #9]) #("Install redis. 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nil nil #14]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #30))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #14]) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #31))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #14]) #("Note for the plant database you can rename it to db" 0 51 (:parent #32)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("webqtl" 0 6 (:parent #36))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("s" 0 1 (:parent #37))) #(", or\nchange the settings in etc/default" 0 39 (:parent #32)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # 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nil nil #11] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #15] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #15))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil (org-data (:standard-properties [1 1 1 15256 15256 0 nil org-data nil nil nil 3 15256 nil # nil nil nil] :path nil :CATEGORY nil) . #0)] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #9))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #9]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #12]) #("See " 0 4 (:parent #15)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #15] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #15))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil (org-data (:standard-properties [1 1 1 15256 15256 0 nil org-data nil nil nil 3 15256 nil # nil nil nil] :path nil :CATEGORY nil) . #0)] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #10))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #10]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #13]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #16)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #16] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #16))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil (org-data (:standard-properties [1 1 1 15256 15256 0 nil org-data nil nil nil 3 15256 nil # nil nil nil] :path nil :CATEGORY nil) . #0)] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #11))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #14))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #14]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #17]) #("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 #20)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #20] :use-brackets-p nil) #("PATH" 0 4 (:parent #24))) #("and R" 0 5 (:parent #20)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #20] :use-brackets-p nil) #("LIBS" 0 4 (:parent #26))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #20] :use-brackets-p nil) #("SITE" 0 4 (:parent #27))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #20))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #17] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("On one system:\n" 0 15 (:parent #22))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #17] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #17]) #("and perhaps a few more.\n" 0 24 (:parent #24))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #15)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #15] :use-brackets-p nil) #("data" 0 4 (:parent #27))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #15)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #15] :use-brackets-p nil) #("files" 0 5 (:parent #29))) #("/genotype'" 0 10 (:parent #15))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #15]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #18]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #21)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #21] :use-brackets-p nil) #("data" 0 4 (:parent #25))) #(". 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 #21)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #21] :use-brackets-p nil) #("settings.py" 0 11 (:parent #27))) #("(see above in\nthis document).\n" 0 30 (:parent #21))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("You can use the GENENETWORK" 0 27 (:parent #22)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #22] :use-brackets-p nil) #("FILES" 0 5 (:parent #26))) #("switch to set the datadir, for example\n" 0 39 (:parent #22))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #18] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #16))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #16]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #19]) #("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 #22))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #17))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #17]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #20]) #("This error\n" 0 11 (:parent #23))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #20] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("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 #25))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #26)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #26] :use-brackets-p nil) #("LIBS" 0 4 (:parent #30))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #26] :use-brackets-p nil) #("SITE" 0 4 (:parent #31))) #(". 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 #26))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #18))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #18]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #21]) #("The following error\n" 0 20 (:parent #24))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #21] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("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 #26))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #21] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #28))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #21] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #30)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #30] :use-brackets-p nil) #("URI" 0 3 (:parent #34))) #("to something like\n" 0 18 (:parent #30))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #21] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil (org-data (:standard-properties [1 1 1 15256 15256 0 nil org-data nil nil nil 3 15256 nil # nil nil nil] :path nil :CATEGORY nil) . #0)] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #12))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #12]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #15]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #18))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #15]) #("#+begin" 0 7 (:parent #19)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #19] :use-brackets-p nil) #("src" 0 3 (:parent #23))) #("\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 #19))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #15]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #20))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #15]) #(" yes\n env GUIX" 0 30 (:parent #21)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #21] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #25))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #21] :use-brackets-p nil) #("PATH" 0 4 (:parent #26))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #21))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #15]) #("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 #22))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #15]) #(" 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 #23)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #23] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #27))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #23] :use-brackets-p nil) #("PATH" 0 4 (:parent #28))) #("=../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 #23))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #15]) #("/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 #24))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #15]) #(" which should have the same HASH values " 0 48 (:parent #25)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #25]) #("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 #29))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #25)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #25] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #25)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #25] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #25)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #25] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #35))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #25] :use-brackets-p nil) #("PATH" 0 4 (:parent #36))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #25)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #25] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #25)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #25] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #40))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #25] :use-brackets-p nil) #("PATH" 0 4 (:parent #41))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #25)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #11)) (link (:standard-properties [1476 nil 1538 1548 1550 0 nil nil nil nil nil nil nil nil # nil nil #11] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #17))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #11))) (paragraph (:standard-properties [1633 1633 1633 1982 1983 1 nil nil nil nil nil nil nil nil # nil nil #8]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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Follow the instructions on\n" 0 117 (:parent #12)) (link (:standard-properties [2247 nil nil nil 2285 1 nil nil nil nil nil nil nil nil # nil nil #12] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #12))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #0] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #7))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #7]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #10]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #13)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #13] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #17)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #17] :use-brackets-p nil) #("settings.py" 0 11 (:parent #21)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #13))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #10] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #10]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #15))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #10] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #10]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #17))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #0] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #8))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #8]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #11]) #("Install redis. 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nil nil #16]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #32))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #33))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("Note for the plant database you can rename it to db" 0 51 (:parent #34)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("webqtl" 0 6 (:parent #38))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("s" 0 1 (:parent #39))) #(", or\nchange the settings in etc/default" 0 39 (:parent #34)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("settings.py" 0 11 (:parent #41))) #("to match your path.\n" 0 20 (:parent #34)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #0] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #10))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #10]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #13]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #16))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #13] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #17] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #17))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #0] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #11))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #11]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #14]) #("See " 0 4 (:parent #17)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #17] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #17))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #0] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #12))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #12]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #15]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #18)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #18] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #18))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #0] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #13))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #13] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #16))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #16]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #19]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #22)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #22] :use-brackets-p nil) #("PATH" 0 4 (:parent #26))) #("and R" 0 5 (:parent #22)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #22] :use-brackets-p nil) #("LIBS" 0 4 (:parent #28))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #22] :use-brackets-p nil) #("SITE" 0 4 (:parent #29))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #22))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #19] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #19]) #("On one system:\n" 0 15 (:parent #24))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #19] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #19]) #("and perhaps a few more.\n" 0 24 (:parent #26))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #13] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #17)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #17] :use-brackets-p nil) #("data" 0 4 (:parent #29))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #17)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #17] :use-brackets-p nil) #("files" 0 5 (:parent #31))) #("/genotype'" 0 10 (:parent #17))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #17]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #20]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #23)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #23] :use-brackets-p nil) #("data" 0 4 (:parent #27))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #23)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #23] :use-brackets-p nil) #("settings.py" 0 11 (:parent #29))) #("(see above in\nthis document).\n" 0 30 (:parent #23))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("You can use the GENENETWORK" 0 27 (:parent #24)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #24] :use-brackets-p nil) #("FILES" 0 5 (:parent #28))) #("switch to set the datadir, for example\n" 0 39 (:parent #24))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #20] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #13] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #18))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #18]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #21]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #24))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #13] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #19))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #19]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #22]) #("This error\n" 0 11 (:parent #25))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #22] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #27))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #28)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #28] :use-brackets-p nil) #("LIBS" 0 4 (:parent #32))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #28] :use-brackets-p nil) #("SITE" 0 4 (:parent #33))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #28))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #13] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #20))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #20]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #23]) #("The following error\n" 0 20 (:parent #26))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #23] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #28))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #23] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #30))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #23] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #32)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("URI" 0 3 (:parent #36))) #("to something like\n" 0 18 (:parent #32))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #23] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #0] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #14))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #14]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #17]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #20))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("#+begin" 0 7 (:parent #21)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #21] :use-brackets-p nil) #("src" 0 3 (:parent #25))) #("\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 #21))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #22))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #17]) #(" yes\n env GUIX" 0 30 (:parent #23)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #23] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #27))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #23] :use-brackets-p nil) #("PATH" 0 4 (:parent #28))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #23))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("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 #24))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #17]) #(" 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 #25)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #25] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #29))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #25] :use-brackets-p nil) #("PATH" 0 4 (:parent #30))) #("=../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 #25))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("/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 #26))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #17]) #(" which should have the same HASH values " 0 48 (:parent #27)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #27]) #("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 #31))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #27)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #27] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #27)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #27] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #27)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #37))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("PATH" 0 4 (:parent #38))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #27)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #27] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #27)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #42))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("PATH" 0 4 (:parent #43))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #27)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #45))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("PATH" 0 4 (:parent #46))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #27)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #27] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #27)))))) (:export-options 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Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #356))))) (headline (:standard-properties [2368 2368 2383 2849 2849 0 (:title) nil nil nil nil 2385 2847 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #351))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2383 2383 2383 2849 2849 0 nil section nil nil nil 2383 2849 nil # nil nil #351]) (paragraph (:standard-properties [2383 2383 2383 2577 2578 1 nil planning nil nil nil nil nil nil # nil nil #354]) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #357)) (link (:standard-properties [2436 nil 2466 2485 2487 0 nil nil nil nil nil nil nil nil # nil nil #357] :type "file" :type-explicit-p nil :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil) #("default" 0 7 (:parent #361)) (subscript (:standard-properties [2473 nil 2474 2485 2485 0 nil nil nil nil nil nil nil nil # nil nil #361] :use-brackets-p nil) #("settings.py" 0 11 (:parent #365)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #357))) (fixed-width (:standard-properties [2578 2578 nil nil 2608 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "genenetwork2 mysettings.py")) (paragraph (:standard-properties [2608 2608 2608 2685 2686 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #359))) (fixed-width (:standard-properties [2686 2686 nil nil 2769 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2")) (paragraph (:standard-properties [2769 2769 2769 2848 2849 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #361))))) (headline (:standard-properties [2849 2849 2866 2931 2931 0 (:title) nil nil nil nil 2868 2929 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 15) t] :title (#("Running Redis" 0 13 (:parent #352))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2866 2866 2866 2931 2931 0 nil section nil nil nil 2866 2931 nil # nil nil #352]) (paragraph (:standard-properties [2866 2866 2866 2912 2913 1 nil planning nil nil nil nil nil nil # nil nil #355]) #("Install redis. Make sure you add the setting:\n" 0 46 (:parent #358))) (fixed-width (:standard-properties [2913 2913 nil nil 2931 2 nil nil nil nil nil nil nil nil # nil nil #355] :value "appendonly yes")))) (headline (:standard-properties [2931 2931 2952 5782 5782 0 (:title) nil nil nil nil 2954 5780 1 # nil nil #344] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #353))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [2952 2952 2986 4250 4250 0 (:title) section nil nil nil 2988 4248 2 # nil nil #353] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #356))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2986 2986 2986 4250 4250 0 nil section nil nil nil 2986 4250 nil # nil nil #356]) (paragraph (:standard-properties [2986 2986 2986 3014 3015 1 nil planning nil nil nil nil nil nil # nil nil #359]) (italic (:standard-properties [2986 nil 2987 3012 3013 0 nil nil nil nil nil nil nil nil # nil nil #362]) #("Note: we moved to MariaDB" 0 25 (:parent #365))) #("\n" 0 1 (:parent #362))) (paragraph (:standard-properties [3015 3015 3015 3151 3152 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #363))) (paragraph (:standard-properties [3152 3152 3152 3178 3179 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("As root configure and run\n" 0 26 (:parent #364))) (src-block (:standard-properties [3179 3179 nil nil 3475 1 nil nil nil nil nil nil nil nil # nil nil #359] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 285) t])) (paragraph (:standard-properties [3475 3475 3475 3522 3523 1 nil nil nil nil nil nil nil nil # 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nil nil #359] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [3872 3872 3872 3949 3950 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #373))) (fixed-width (:standard-properties [3950 3950 nil nil 4060 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [4060 4060 4060 4086 4087 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("When you get errors like:\n" 0 26 (:parent #375))) (fixed-width (:standard-properties [4087 4087 nil nil 4201 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [4201 4201 4201 4221 4222 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("you may need to set\n" 0 20 (:parent #377))) (fixed-width (:standard-properties [4222 4222 nil nil 4250 2 nil nil nil nil nil nil nil nil # nil nil #359] :value "set foreign_key_checks=0")))) (headline (:standard-properties [4250 4250 4287 5782 5782 0 (:title) nil nil nil nil 4289 5780 2 # nil nil #353] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #357))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4287 4287 4287 5782 5782 0 nil section nil nil nil 4287 5782 nil # nil nil #357]) (paragraph (:standard-properties [4287 4287 4287 4593 4594 1 nil planning nil nil nil nil nil nil # nil nil #360]) #("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 #363)) (subscript (:standard-properties [4450 nil 4451 4457 4457 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("webqtl" 0 6 (:parent #367))) (subscript (:standard-properties [4457 nil 4458 4459 4459 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("s" 0 1 (:parent #368))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #363)) (subscript (:standard-properties [4535 nil 4536 4542 4542 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("webqtl" 0 6 (:parent #370))) (subscript (:standard-properties [4542 nil 4543 4548 4548 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("plant" 0 5 (:parent #371))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #363))) (paragraph (:standard-properties [4594 4594 4594 4621 4622 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Download one database from\n" 0 27 (:parent #364))) (paragraph (:standard-properties [4622 4622 4622 4669 4670 1 nil nil nil nil nil nil nil nil # nil nil #360]) (link (:standard-properties [4622 nil nil nil 4668 0 nil nil nil nil nil nil nil nil # nil nil #365] :type "http" :type-explicit-p t :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil)) #("\n" 0 1 (:parent #365))) (paragraph (:standard-properties [4670 4670 4670 4728 4729 1 nil nil nil nil nil nil nil nil # nil nil #360]) (link (:standard-properties [4670 nil nil nil 4727 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :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)) #("\n" 0 1 (:parent #366))) (paragraph (:standard-properties [4729 4729 4729 4747 4748 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Check the md5sum.\n" 0 18 (:parent #367))) (paragraph (:standard-properties [4748 4748 4748 4818 4819 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #368))) (fixed-width (:standard-properties [4819 4819 nil nil 4920 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*")) (paragraph (:standard-properties [4920 4920 4920 4966 4967 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #370))) (fixed-width (:standard-properties [4967 4967 nil nil 4984 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "myslq -u root")) (paragraph (:standard-properties [4984 4984 4984 4988 4989 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("and\n" 0 4 (:parent #372))) (fixed-width (:standard-properties [4989 4989 nil nil 5215 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [5215 5215 5215 5279 5280 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #374))) (fixed-width (:standard-properties [5280 5280 nil nil 5379 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';")) (paragraph (:standard-properties [5379 5379 5379 5485 5486 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #376))) (paragraph (:standard-properties [5486 5486 5486 5648 5649 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("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 #377))) (paragraph (:standard-properties [5649 5649 5649 5781 5782 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Note for the plant database you can rename it to db" 0 51 (:parent #378)) (subscript (:standard-properties [5700 nil 5701 5707 5707 0 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("webqtl" 0 6 (:parent #382))) (subscript (:standard-properties [5707 nil 5708 5709 5709 0 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("s" 0 1 (:parent #383))) #(", or\nchange the settings in etc/default" 0 39 (:parent #378)) (subscript (:standard-properties [5748 nil 5749 5760 5761 1 nil nil nil nil nil nil nil nil # nil nil #378] :use-brackets-p nil) #("settings.py" 0 11 (:parent #385))) #("to match your path.\n" 0 20 (:parent #378)))))) (headline (:standard-properties [5782 5782 5806 5946 5946 0 (:title) nil nil nil nil 5808 5944 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #354))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5806 5806 5806 5946 5946 0 nil section nil nil nil 5806 5946 nil # nil nil #354]) (paragraph (:standard-properties [5806 5806 5806 5866 5867 1 nil planning nil nil nil nil nil nil # nil nil #357]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #360))) (paragraph (:standard-properties [5867 5897 5897 5945 5946 1 nil nil nil nil nil nil nil nil # nil nil #357] :attr_html (":title GN2_graph")) (link (:standard-properties [5897 nil nil nil 5944 0 nil nil nil nil nil nil nil nil # nil nil #361] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #361))))) (headline (:standard-properties [5946 5946 5982 6008 6008 0 (:title) nil nil nil nil 5984 6006 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #355))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5982 5982 5982 6008 6008 0 nil section nil nil nil 5982 6008 nil # nil nil #355]) (paragraph (:standard-properties [5982 5982 5982 6007 6008 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("See " 0 4 (:parent #361)) (link (:standard-properties [5986 nil nil nil 6005 0 nil nil nil nil nil nil nil nil # nil nil #361] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #361))))) (headline (:standard-properties [6008 6008 6021 6158 6158 0 (:title) nil nil nil nil 6023 6156 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #356))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6021 6021 6021 6158 6158 0 nil section nil nil nil 6021 6158 nil # nil nil #356]) (paragraph (:standard-properties [6021 6021 6021 6157 6158 1 nil planning nil nil nil nil nil nil # nil nil #359]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #362)) (link (:standard-properties [6076 nil nil nil 6096 0 nil nil nil nil nil nil nil nil # nil nil #362] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #362))))) (headline (:standard-properties [6158 6158 6178 8609 8609 0 (:title) nil nil nil nil 6180 8607 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #357))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6178 6178 6218 6712 6712 0 (:title) section nil nil nil 6220 6710 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #360))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 6712 6712 0 nil section nil nil nil 6218 6712 nil # nil nil #360]) (paragraph (:standard-properties [6218 6218 6218 6452 6453 1 nil planning nil nil nil nil nil nil # nil nil #363]) #("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 #366)) (subscript (:standard-properties [6385 nil 6386 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("PATH" 0 4 (:parent #370))) #("and R" 0 5 (:parent #366)) (subscript (:standard-properties [6396 nil 6397 6401 6401 0 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("LIBS" 0 4 (:parent #372))) (subscript (:standard-properties [6401 nil 6402 6406 6407 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("SITE" 0 4 (:parent #373))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #366))) (fixed-width (:standard-properties [6453 6453 nil nil 6484 2 nil nil nil nil nil nil nil nil # nil nil #363] :value "guix package --search-paths")) (paragraph (:standard-properties [6484 6484 6484 6499 6500 1 nil nil nil nil nil nil nil nil # nil nil #363]) #("On one system:\n" 0 15 (:parent #368))) (fixed-width (:standard-properties [6500 6500 nil nil 6688 2 nil nil nil nil nil nil nil nil # nil nil #363] :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\"")) (paragraph (:standard-properties [6688 6688 6688 6712 6712 0 nil nil nil nil nil nil nil nil # nil nil #363]) #("and perhaps a few more.\n" 0 24 (:parent #370))))) (headline (:standard-properties [6712 6712 6821 7208 7208 0 (:title) nil nil nil nil 6823 7206 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #361)) (subscript (:standard-properties [6755 nil 6756 6760 6760 0 nil nil nil nil nil nil nil nil # nil nil #361] :use-brackets-p nil) #("data" 0 4 (:parent #373))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #361)) (subscript (:standard-properties [6803 nil 6804 6809 6809 0 nil nil nil nil nil nil nil nil # nil nil #361] :use-brackets-p nil) #("files" 0 5 (:parent #375))) #("/genotype'" 0 10 (:parent #361))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6821 6821 6821 7208 7208 0 nil section nil nil nil 6821 7208 nil # nil nil #361]) (paragraph (:standard-properties [6821 6821 6821 7042 7043 1 nil planning nil nil nil nil nil nil # nil nil #364]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #367)) (subscript (:standard-properties [6870 nil 6871 6875 6875 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("data" 0 4 (:parent #371))) #(". 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 #367)) (subscript (:standard-properties [6999 nil 7000 7011 7012 1 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("settings.py" 0 11 (:parent #373))) #("(see above in\nthis document).\n" 0 30 (:parent #367))) (paragraph (:standard-properties [7043 7043 7043 7116 7117 1 nil nil nil nil nil nil nil nil # nil nil #364]) #("You can use the GENENETWORK" 0 27 (:parent #368)) (subscript (:standard-properties [7070 nil 7071 7076 7077 1 nil nil nil nil nil nil nil nil # nil nil #368] :use-brackets-p nil) #("FILES" 0 5 (:parent #372))) #("switch to set the datadir, for example\n" 0 39 (:parent #368))) (fixed-width (:standard-properties [7117 7117 nil nil 7208 2 nil nil nil nil nil nil nil nil # nil nil #364] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [7208 7208 7231 7442 7442 0 (:title) nil nil nil nil 7233 7440 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #362))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7231 7231 7231 7442 7442 0 nil section nil nil nil 7231 7442 nil # nil nil #362]) (paragraph (:standard-properties [7231 7231 7231 7442 7442 0 nil planning nil nil nil nil nil nil # nil nil #365]) #("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 #368))))) (headline (:standard-properties [7442 7442 7474 7943 7943 0 (:title) nil nil nil nil 7476 7941 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #363))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7474 7474 7474 7943 7943 0 nil section nil nil nil 7474 7943 nil # nil nil #363]) (paragraph (:standard-properties [7474 7474 7474 7485 7486 1 nil planning nil nil nil nil nil nil # nil nil #366]) #("This error\n" 0 11 (:parent #369))) (fixed-width (:standard-properties [7486 7486 nil nil 7566 2 nil nil nil nil nil nil nil nil # nil nil #366] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [7566 7566 7566 7696 7697 1 nil nil nil nil nil nil nil nil # nil nil #366]) #("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 #371))) (paragraph (:standard-properties [7697 7697 7697 7942 7943 1 nil nil nil nil nil nil nil nil # nil nil #366]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #372)) (subscript (:standard-properties [7760 nil 7761 7765 7765 0 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("LIBS" 0 4 (:parent #376))) (subscript (:standard-properties [7765 nil 7766 7770 7770 0 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("SITE" 0 4 (:parent #377))) #(". 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 #372))))) (headline (:standard-properties [7943 7943 7995 8609 8609 0 (:title) nil nil nil nil 7997 8607 2 # nil nil #357] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #364))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7995 7995 7995 8609 8609 0 nil section nil nil nil 7995 8609 nil # nil nil #364]) (paragraph (:standard-properties [7995 7995 7995 8015 8016 1 nil planning nil nil nil nil nil nil # nil nil #367]) #("The following error\n" 0 20 (:parent #370))) (fixed-width (:standard-properties [8016 8016 nil nil 8211 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')")) (paragraph (:standard-properties [8211 8211 8211 8368 8369 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("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 #372))) (fixed-width (:standard-properties [8369 8369 nil nil 8391 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "mysql -h localhost")) (paragraph (:standard-properties [8391 8391 8391 8447 8448 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #374))) (fixed-width (:standard-properties [8448 8448 nil nil 8470 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [8470 8470 8470 8540 8541 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #376)) (subscript (:standard-properties [8517 nil 8518 8521 8522 1 nil nil nil nil nil nil nil nil # nil nil #376] :use-brackets-p nil) #("URI" 0 3 (:parent #380))) #("to something like\n" 0 18 (:parent #376))) (fixed-width (:standard-properties [8541 8541 nil nil 8609 3 nil nil nil nil nil nil nil nil # nil nil #367] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [8609 8609 8624 15256 15256 0 (:title) nil nil nil nil 8626 15254 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("IRC session" 0 11 (:parent #358))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [8624 8624 8624 15256 15256 0 nil section nil nil nil 8624 15256 nil # nil nil #358]) (paragraph (:standard-properties [8624 8624 8624 8732 8733 1 nil planning nil nil nil nil nil nil # nil nil #361]) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #364))) (paragraph (:standard-properties [8733 8733 8733 9293 9294 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("#+begin" 0 7 (:parent #365)) (subscript (:standard-properties [8740 nil 8741 8744 8744 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("src" 0 3 (:parent #369))) #("\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 #365))) (paragraph (:standard-properties [9294 9294 9294 9383 9384 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #366))) (paragraph (:standard-properties [9384 9384 9384 9528 9529 1 nil nil nil nil nil nil nil nil # nil nil #361]) #(" yes\n env GUIX" 0 30 (:parent #367)) (subscript (:standard-properties [9414 nil 9415 9422 9422 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #371))) (subscript (:standard-properties [9422 nil 9423 9427 9427 0 nil nil nil nil nil nil nil nil # nil nil #367] :use-brackets-p nil) #("PATH" 0 4 (:parent #372))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #367))) (paragraph (:standard-properties [9529 9529 9529 9824 9825 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("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 #368))) (paragraph (:standard-properties [9825 9825 9825 11017 11018 1 nil nil nil nil nil nil nil nil # nil nil #361]) #(" 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 #369)) (subscript (:standard-properties [10578 nil 10579 10586 10586 0 nil nil nil nil nil nil nil nil # nil nil #369] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #373))) (subscript (:standard-properties [10586 nil 10587 10591 10591 0 nil nil nil nil nil nil nil nil # nil nil #369] :use-brackets-p nil) #("PATH" 0 4 (:parent #374))) #("=../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 #369))) (paragraph (:standard-properties [11018 11018 11018 11221 11222 1 nil nil nil nil nil nil nil nil # nil nil #361]) #("/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 #370))) (paragraph (:standard-properties [11222 11222 11222 15256 15256 0 nil nil nil nil nil nil nil nil # nil nil #361]) #(" which should have the same HASH values " 0 48 (:parent #371)) (italic (:standard-properties [11270 nil 11271 12178 12179 0 nil nil nil nil nil nil nil nil # nil nil #371]) #("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 #375))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #371)) (link (:standard-properties [12979 nil nil nil 13044 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #371)) (link (:standard-properties [13292 nil nil nil 13325 1 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #371)) (subscript (:standard-properties [13549 nil 13550 13557 13557 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #381))) (subscript (:standard-properties [13557 nil 13558 13562 13562 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #382))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #371)) (link (:standard-properties [13678 nil nil nil 13705 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #371)) (subscript (:standard-properties [14275 nil 14276 14283 14283 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #386))) (subscript (:standard-properties [14283 nil 14284 14288 14288 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #387))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #371)) (subscript (:standard-properties [14947 nil 14948 14955 14955 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #389))) (subscript (:standard-properties [14955 nil 14956 14960 14960 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("PATH" 0 4 (:parent #390))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #371)) (link (:standard-properties [15074 nil nil nil 15106 0 nil nil nil nil nil nil nil nil # nil nil #371] :type "http" :type-explicit-p t :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #371)))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) org-export-as(html nil nil t nil) org-export-to-buffer(html "*Org HTML Export*" nil nil nil t nil #f(compiled-function () #)) org-html-export-as-html(nil nil nil t) (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (unwind-protect (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer))) (save-current-buffer (set-buffer temp-buffer) (unwind-protect (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer)))) (let ((temp-buffer (generate-new-buffer " *temp*" t))) (save-current-buffer (set-buffer temp-buffer) (unwind-protect (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer))))) eval-buffer(# nil "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el" nil t) #f(compiled-function (buffer file) #)(# "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el") load-with-code-conversion("/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el" "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el" nil t #f(compiled-function (buffer file) #)) command-line--load-script("/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el") command-line-1(("-scriptload" "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el")) command-line() normal-top-level()
generated by cgit-pink 1.4.1 (git 2.36.1) at 2026-02-07 08:33:53 +0000