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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. Unable to resolve link: %S\nSee `org-export-with-broken-links'" "introduction") org-export-data((link (:standard-properties [138 nil 155 167 169 0 nil nil nil nil nil nil nil nil # nil nil (paragraph (:standard-properties [138 138 138 170 170 0 nil nil nil nil nil nil nil nil # nil nil (item (:standard-properties [135 135 138 170 170 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 616) (249 3 "- " nil nil nil 312) (312 3 "- " nil nil nil 372) (372 3 "- " nil nil nil 466) (466 3 "- " nil nil nil 550) (550 3 "- " nil nil nil 616) (616 1 "- " nil nil nil 671) (671 1 "- " nil nil nil 710) (710 1 "- " nil nil nil 885) (755 3 "- " nil nil nil 816) (816 3 "- " nil nil nil 885) (885 1 "- " nil nil nil 1129) (1012 3 "- " nil nil nil 1067) (1067 3 "- " nil nil nil 1102) (1102 3 "- " nil nil nil 1129)) (plain-list (:standard-properties [135 135 135 1129 1130 1 nil planning nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 616) (249 3 "- " nil nil nil 312) (312 3 "- " nil nil nil 372) (372 3 "- " nil nil nil 466) (466 3 "- " nil nil nil 550) (550 3 "- " nil nil nil 616) (616 1 "- " nil nil nil 671) (671 1 "- " nil nil nil 710) (710 1 "- " nil nil nil 885) (755 3 "- " nil nil nil 816) (816 3 "- " nil nil nil 885) (885 1 "- " nil nil nil 1129) (1012 3 "- " nil nil nil 1067) (1067 3 "- " nil nil nil 1102) (1102 3 "- " nil nil nil 1129)) (section (:standard-properties [135 135 135 1130 1130 0 nil section nil nil nil 135 1130 nil # nil nil (headline (:standard-properties [57 57 135 1130 1130 0 (:title) nil nil nil nil 137 1128 1 # nil nil (org-data (:standard-properties [1 1 1 13393 13393 0 nil org-data nil nil nil 3 13393 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 57 57 0 nil first-section nil nil nil 1 57 nil # nil nil #30]) (keyword (:standard-properties [1 1 nil nil 57 1 nil top-comment nil nil nil nil nil nil # nil nil #33] :key "TITLE" :value "Installing GeneNetwork services with GNU Guix"))) #25 (headline (:standard-properties [1130 1130 1146 1409 1409 0 (:title) nil nil nil nil 1148 1407 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 [1146 1146 1146 1409 1409 0 nil section nil nil nil 1146 1409 nil # nil nil #35]) (paragraph (:standard-properties [1146 1146 1146 1408 1409 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Large system deployments tend to get very complex. In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #41)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #45))) #("and the main " 0 13 (:parent #41)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #41] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #41))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #30] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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 [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #36] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (: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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #39]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #42]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #45))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. If you use a virtual machine we recommend to use at least\ndouble.\n" 0 141 (:parent #46))))) (headline (:standard-properties [1928 1928 1957 3555 3555 0 (:title) nil nil nil nil 1959 3553 2 # nil nil #36] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 27) t] :title (#("Step 1: Install GNU Guix" 0 24 (: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 [1957 1957 1957 3555 3555 0 nil section nil nil nil 1957 3555 nil # nil nil #40]) (paragraph (:standard-properties [1957 1957 1957 2409 2410 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("Fetch the GNU Guix binary from " 0 31 (:parent #46)) (link (:standard-properties [1988 nil 2035 2039 2042 1 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/download/" :format bracket :raw-link "https://www.gnu.org/software/guix/download/" :application nil :search-option nil) #("here" 0 4 (:parent #50))) #("(middle panel) and follow\n" 0 26 (:parent #46)) (link (:standard-properties [2068 nil 2147 2159 2161 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :format bracket :raw-link "https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :application nil :search-option nil) #("instructions" 0 12 (:parent #52))) #(". Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #46))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Once you have succeeded, you have to " 0 37 (:parent #47)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #51))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #47))) (src-block (:standard-properties [2688 2688 nil nil 2796 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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Which should show something like\n" 0 33 (:parent #49))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #43] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) (paragraph (:standard-properties [2940 2940 2940 2950 2951 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("#+end" 0 5 (:parent #51)) (subscript (:standard-properties [2945 nil 2946 2949 2949 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("src" 0 3 (:parent #55))) #("\n" 0 1 (:parent #51))) (paragraph (:standard-properties [2951 2951 2951 3021 3022 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("means binary installs. The actual installation command of 'hello' is\n" 0 70 (:parent #52))) (src-block (:standard-properties [3022 3022 nil nil 3094 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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #54))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("If you need more help we have another writeup in " 0 49 (:parent #55)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #59))) #(". To get\nrid of the locale warning see " 0 39 (:parent #55)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #61))) #(".\n" 0 2 (:parent #55))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #36] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #41]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #47))) (src-block (:standard-properties [3721 3721 nil nil 3826 1 nil nil nil nil nil nil nil nil # nil nil #44] :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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #49))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("#+begin" 0 7 (:parent #50)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("src" 0 3 (:parent #54))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #50)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #50] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #50)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #50] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #50)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("src" 0 3 (:parent #60))) #("bash\n" 0 5 (:parent #50))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("To test whether this is working try:\n" 0 37 (:parent #51))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("#+begin" 0 7 (:parent #52)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("src" 0 3 (:parent #56))) #("bash\n#+end" 0 10 (:parent #52)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("src" 0 3 (:parent #58))) #("bash\n" 0 5 (:parent #52))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #36] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #42]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #48))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #45] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("by pasting it into the command\n" 0 31 (:parent #50))) (src-block (:standard-properties [4526 4526 nil nil 4579 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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("and hit Ctrl-D.\n" 0 16 (:parent #52))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #53))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #36] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #43]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #49))) (src-block (:standard-properties [4832 4832 nil nil 4951 1 nil nil nil nil nil nil nil nil # nil nil #46] :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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #51))) (src-block (:standard-properties [5004 5004 nil nil 5194 1 nil nil nil nil nil nil nil nil # nil nil #46] :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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #53)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #53]) #("root" 0 4 (:parent #57))) #(".config/guix/latest override).\n" 0 31 (:parent #53))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("And install with\n" 0 17 (:parent #54))) (src-block (:standard-properties [5321 5321 nil nil 5491 1 nil nil nil nil nil nil nil nil # nil nil #46] :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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #56))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #57))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #58))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #46] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #60))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #46] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #62)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #62] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #62))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #63)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #37]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("GNU Guix allows for " 0 20 (:parent #43)) (link (:standard-properties [6584 nil 6653 6676 6679 1 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 bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #47))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #43))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #40] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #45)) (link (:standard-properties [7007 nil 7112 7122 7124 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #49))) #(".\n" 0 2 (:parent #45))) (paragraph (:standard-properties [7127 7127 7127 7190 7191 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #46))) (fixed-width (:standard-properties [7191 7191 nil nil 7247 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [7247 7247 7247 7250 7251 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("So\n" 0 3 (:parent #48))) (paragraph (:standard-properties [7251 7251 7251 7637 7638 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("#+begin" 0 7 (:parent #49)) (subscript (:standard-properties [7258 nil 7259 7262 7263 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("src" 0 3 (:parent #53))) #("sh :lang bash\n#+begin" 0 23 (:parent #49)) (subscript (:standard-properties [7286 nil 7287 7290 7291 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("src" 0 3 (:parent #55))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #49)) (subscript (:standard-properties [7331 nil 7332 7339 7339 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #57))) (subscript (:standard-properties [7339 nil 7340 7344 7344 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PATH" 0 4 (:parent #58))) #("=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork\ngenenetwork1 1.0-d622c803b out ../guix-bioinformatics/gn/packages/bioinformatics.scm:163:2\ngenenetwork2 2.0-9e9475053 out ../guix-bioinformatics/gn/packages/bioinformatics.scm:215:2\n#+end" 0 272 (:parent #49)) (subscript (:standard-properties [7616 nil 7617 7620 7621 1 nil nil nil nil nil nil nil nil # 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nil nil #352]) #("Large system deployments tend to get very complex. In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #355)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #359))) #("and the main " 0 13 (:parent #355)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #355] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #355))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #344] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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) (headline (:standard-properties [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (:parent #353))) :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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #353]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #356]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #359))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. If you use a virtual machine we recommend to use at least\ndouble.\n" 0 141 (:parent #360))))) (headline (:standard-properties [1928 1928 1957 3555 3555 0 (:title) nil nil nil nil 1959 3553 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 27) t] :title (#("Step 1: Install GNU Guix" 0 24 (:parent #354))) :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 [1957 1957 1957 3555 3555 0 nil section nil nil nil 1957 3555 nil # nil nil #354]) (paragraph (:standard-properties [1957 1957 1957 2409 2410 1 nil planning nil nil nil nil nil nil # nil nil #357]) #("Fetch the GNU Guix binary from " 0 31 (:parent #360)) (link (:standard-properties [1988 nil 2035 2039 2042 1 nil nil nil nil nil nil nil nil # nil nil #360] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/download/" :format bracket :raw-link "https://www.gnu.org/software/guix/download/" :application nil :search-option nil) #("here" 0 4 (:parent #364))) #("(middle panel) and follow\n" 0 26 (:parent #360)) (link (:standard-properties [2068 nil 2147 2159 2161 0 nil nil nil nil nil nil nil nil # nil nil #360] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :format bracket :raw-link "https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :application nil :search-option nil) #("instructions" 0 12 (:parent #366))) #(". Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #360))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("Once you have succeeded, you have to " 0 37 (:parent #361)) (link (:standard-properties [2447 nil 2523 2534 2537 1 nil nil nil nil nil nil nil nil # nil nil #361] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #365))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #361))) (src-block (:standard-properties [2688 2688 nil nil 2796 1 nil nil nil nil nil nil nil nil # nil nil #357] :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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("Which should show something like\n" 0 33 (:parent #363))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #357] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) (paragraph (:standard-properties [2940 2940 2940 2950 2951 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("#+end" 0 5 (:parent #365)) (subscript (:standard-properties [2945 nil 2946 2949 2949 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("src" 0 3 (:parent #369))) #("\n" 0 1 (:parent #365))) (paragraph (:standard-properties [2951 2951 2951 3021 3022 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("means binary installs. The actual installation command of 'hello' is\n" 0 70 (:parent #366))) (src-block (:standard-properties [3022 3022 nil nil 3094 1 nil nil nil nil nil nil nil nil # nil nil #357] :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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #368))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("If you need more help we have another writeup in " 0 49 (:parent #369)) (link (:standard-properties [3330 nil 3414 3424 3426 0 nil nil nil nil nil nil nil nil # nil nil #369] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #373))) #(". To get\nrid of the locale warning see " 0 39 (:parent #369)) (link (:standard-properties [3465 nil 3540 3550 3552 0 nil nil nil nil nil nil nil nil # nil nil #369] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #375))) #(".\n" 0 2 (:parent #369))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (:parent #355))) :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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #355]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #361))) (src-block (:standard-properties [3721 3721 nil nil 3826 1 nil nil nil nil nil nil nil nil # nil nil #358] :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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #363))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("#+begin" 0 7 (:parent #364)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #364] :use-brackets-p nil) #("src" 0 3 (:parent #368))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #364)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #364] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #364)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #364] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #364)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #364] :use-brackets-p nil) #("src" 0 3 (:parent #374))) #("bash\n" 0 5 (:parent #364))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("To test whether this is working try:\n" 0 37 (:parent #365))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("#+begin" 0 7 (:parent #366)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("src" 0 3 (:parent #370))) #("bash\n#+end" 0 10 (:parent #366)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("src" 0 3 (:parent #372))) #("bash\n" 0 5 (:parent #366))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #356]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #359]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #362))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #359] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("by pasting it into the command\n" 0 31 (:parent #364))) (src-block (:standard-properties [4526 4526 nil nil 4579 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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("and hit Ctrl-D.\n" 0 16 (:parent #366))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #367))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 0 27 (: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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #357]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #360]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #363))) (src-block (:standard-properties [4832 4832 nil nil 4951 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #365))) (src-block (:standard-properties [5004 5004 nil nil 5194 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #367)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #367]) #("root" 0 4 (:parent #371))) #(".config/guix/latest override).\n" 0 31 (:parent #367))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("And install with\n" 0 17 (:parent #368))) (src-block (:standard-properties [5321 5321 nil nil 5491 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #370))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #371))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #372))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #374))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #376)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #376] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #376))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #377)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #351]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #354]) #("GNU Guix allows for " 0 20 (:parent #357)) (link (:standard-properties [6584 nil 6653 6676 6679 1 nil nil nil nil nil nil nil nil # nil nil #357] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #361))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #357))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #354] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #359)) (link (:standard-properties [7007 nil 7112 7122 7124 0 nil nil nil nil nil nil nil nil # nil nil #359] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #363))) #(".\n" 0 2 (:parent #359))) (paragraph (:standard-properties [7127 7127 7127 7190 7191 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #360))) (fixed-width (:standard-properties [7191 7191 nil nil 7247 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [7247 7247 7247 7250 7251 1 nil nil nil nil nil nil nil nil # 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Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #46))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Once you have succeeded, you have to " 0 37 (:parent #47)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #51))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #47))) (src-block (:standard-properties [2688 2688 nil nil 2796 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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Which should show something like\n" 0 33 (:parent #49))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #43] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) 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Press Ctrl-C to interrupt.\n" 0 186 (:parent #54))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("If you need more help we have another writeup in " 0 49 (:parent #55)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #59))) #(". To get\nrid of the locale warning see " 0 39 (:parent #55)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #61))) #(".\n" 0 2 (:parent #55))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #36] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #41]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #47))) (src-block (:standard-properties [3721 3721 nil nil 3826 1 nil nil nil nil nil nil nil nil # nil nil #44] :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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #49))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("#+begin" 0 7 (:parent #50)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("src" 0 3 (:parent #54))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #50)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #50] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #50)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #50] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #50)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("src" 0 3 (:parent #60))) #("bash\n" 0 5 (:parent #50))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("To test whether this is working try:\n" 0 37 (:parent #51))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("#+begin" 0 7 (:parent #52)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("src" 0 3 (:parent #56))) #("bash\n#+end" 0 10 (:parent #52)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("src" 0 3 (:parent #58))) #("bash\n" 0 5 (:parent #52))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #36] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #42]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("GN2 has its own GNU Guix binary distribution server. 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The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #57))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #58))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #46] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #60))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #46] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #62)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #62] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #62))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #63)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #37]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("GNU Guix allows for " 0 20 (:parent #43)) (link (:standard-properties [6584 nil 6653 6676 6679 1 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 bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #47))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #43))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #40] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # 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These settings may\nnot reflect your system. To override settings create your own from a copy of\ndefault" 0 105 (:parent #54)) (subscript (:standard-properties [9068 nil 9069 9080 9081 1 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("settings.py" 0 11 (:parent #62))) #("and pass it into GN2 with\n" 0 26 (:parent #54))) (fixed-width (:standard-properties [9108 9108 nil nil 9151 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "./bin/genenetwork2 $HOME/my_settings.py")) (paragraph (:standard-properties [9151 9151 9151 9296 9297 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("and everything " 0 15 (:parent #56)) (bold (:standard-properties [9166 nil 9167 9173 9175 1 nil nil nil nil nil nil nil nil # nil nil #56]) #("should" 0 6 (:parent #60))) #("work (note the full path to the settings\nfile). 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Essentially\nthe configuration looks like\n" 0 167 (:parent #50))) (paragraph (:standard-properties [9728 9728 9728 9867 9868 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("#+begin" 0 7 (:parent #51)) (subscript (:standard-properties [9735 nil 9736 9739 9740 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("src" 0 3 (:parent #55))) #("js\n server {\n listen 80;\n server" 0 49 (:parent #51)) (subscript (:standard-properties [9789 nil 9790 9794 9795 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("name" 0 4 (:parent #57))) #("test-gn2.genenetwork.org;\n access" 0 40 (:parent #51)) (subscript (:standard-properties [9835 nil 9836 9839 9841 2 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("log" 0 3 (:parent #59))) #("logs/test-gn2.access.log;\n" 0 26 (:parent #51))) (paragraph (:standard-properties [9868 9868 9868 10036 10037 1 nil nil nil nil nil nil nil nil # nil nil #47]) #(" proxy" 0 13 (:parent #52)) (subscript (:standard-properties [9881 nil 9882 9889 9889 0 nil nil nil nil nil nil nil nil # 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A configuration file for\nGeneNetwork (reverse proxy) port forwarding can be found in the source\nrepository under ./etc/nginx-genenetwork.conf. Copy this file to /etc\n(still as root)\n" 0 226 (:parent #60))) (fixed-width (:standard-properties [11404 11404 nil nil 11451 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "cp ./etc/nginx-genenetwork.conf /etc/nginx/")) (paragraph (:standard-properties [11451 11451 11451 11461 11462 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Make dirs\n" 0 10 (:parent #62))) (fixed-width (:standard-properties [11462 11462 nil nil 11496 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "mkdir -p /var/spool/nginx/logs")) (paragraph (:standard-properties [11496 11496 11496 11506 11507 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Add users\n" 0 10 (:parent #64))) (fixed-width (:standard-properties [11507 11507 nil nil 11543 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "adduser nobody ; addgroup nobody")) (paragraph (:standard-properties [11543 11543 11543 11553 11554 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Run nginx\n" 0 10 (:parent #66))) (fixed-width (:standard-properties [11554 11554 nil nil 11645 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "/root/.guix-profile/sbin/nginx -c /etc/nginx/nginx-genenetwork.conf -p /var/spool/nginx"))))) (headline (:standard-properties [11645 11645 11707 13393 13393 0 (:title) nil nil nil nil 11709 13391 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 60) t] :title (#("Source deployment and other information on reproducibility" 0 58 (: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 [11707 11707 11707 11764 11764 0 nil section nil nil nil 11707 11764 nil # nil nil #40]) (paragraph (:standard-properties [11707 11707 11707 11763 11764 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("See the document " 0 17 (:parent #46)) (link (:standard-properties [11724 nil nil nil 11761 0 nil nil nil nil nil nil nil nil # nil nil #46] :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)) #(".\n" 0 2 (:parent #46)))) (headline (:standard-properties [11764 11764 11790 12214 12214 0 (:title) nil nil nil nil 11792 12212 2 # nil nil #40] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 24) t] :title (#("Update to recent guix" 0 21 (: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 [11790 11790 11790 12214 12214 0 nil section nil nil nil 11790 12214 nil # nil nil #44]) (paragraph (:standard-properties [11790 11790 11790 11824 11825 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("We now compile Guix from scratch.\n" 0 34 (:parent #50))) (paragraph (:standard-properties [11825 11825 11825 12099 12100 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Create, install and run a recent version of the guix-daemon by\ncompiling the guix repository you have installed with git in\nstep 2. 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In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #42)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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/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))) #("and the main " 0 13 (:parent #42)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #42] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #42))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #31] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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 [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (: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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #40]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #43]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #46))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. If you use a virtual machine we recommend to use at least\ndouble.\n" 0 141 (:parent #47))))) (headline (:standard-properties [1928 1928 1957 3555 3555 0 (:title) nil nil nil nil 1959 3553 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 27) t] :title (#("Step 1: Install GNU Guix" 0 24 (: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 [1957 1957 1957 3555 3555 0 nil section nil nil nil 1957 3555 nil # nil nil #41]) (paragraph (:standard-properties [1957 1957 1957 2409 2410 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("Fetch the GNU Guix binary from " 0 31 (:parent #47)) (link (:standard-properties [1988 nil 2035 2039 2042 1 nil nil nil nil nil nil nil nil # nil nil #47] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/download/" :format bracket :raw-link "https://www.gnu.org/software/guix/download/" :application nil :search-option nil) #("here" 0 4 (:parent #51))) #("(middle panel) and follow\n" 0 26 (:parent #47)) (link (:standard-properties [2068 nil 2147 2159 2161 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :format bracket :raw-link "https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :application nil :search-option nil) #("instructions" 0 12 (:parent #53))) #(". Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #47))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Once you have succeeded, you have to " 0 37 (:parent #48)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #52))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #48))) (src-block (:standard-properties [2688 2688 nil nil 2796 1 nil nil nil nil nil nil nil nil # nil nil #44] :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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Which should show something like\n" 0 33 (:parent #50))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #44] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) (paragraph (:standard-properties [2940 2940 2940 2950 2951 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("#+end" 0 5 (:parent #52)) (subscript (:standard-properties [2945 nil 2946 2949 2949 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("src" 0 3 (:parent #56))) #("\n" 0 1 (:parent #52))) (paragraph (:standard-properties [2951 2951 2951 3021 3022 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("means binary installs. The actual installation command of 'hello' is\n" 0 70 (:parent #53))) (src-block (:standard-properties [3022 3022 nil nil 3094 1 nil nil nil nil nil nil nil nil # nil nil #44] :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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #55))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("If you need more help we have another writeup in " 0 49 (:parent #56)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #60))) #(". To get\nrid of the locale warning see " 0 39 (:parent #56)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #62))) #(".\n" 0 2 (:parent #56))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #42]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #48))) (src-block (:standard-properties [3721 3721 nil nil 3826 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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #50))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("#+begin" 0 7 (:parent #51)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("src" 0 3 (:parent #55))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #51)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #51)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #51] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #51)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("src" 0 3 (:parent #61))) #("bash\n" 0 5 (:parent #51))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("To test whether this is working try:\n" 0 37 (:parent #52))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("#+begin" 0 7 (:parent #53)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("src" 0 3 (:parent #57))) #("bash\n#+end" 0 10 (:parent #53)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("src" 0 3 (:parent #59))) #("bash\n" 0 5 (:parent #53))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #43]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #49))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #46] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("by pasting it into the command\n" 0 31 (:parent #51))) (src-block (:standard-properties [4526 4526 nil nil 4579 1 nil nil nil nil nil nil nil nil # nil nil #46] :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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("and hit Ctrl-D.\n" 0 16 (:parent #53))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #54))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #44]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #50))) (src-block (:standard-properties [4832 4832 nil nil 4951 1 nil nil nil nil nil nil nil nil # nil nil #47] :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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #52))) (src-block (:standard-properties [5004 5004 nil nil 5194 1 nil nil nil nil nil nil nil nil # nil nil #47] :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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #54)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #54]) #("root" 0 4 (:parent #58))) #(".config/guix/latest override).\n" 0 31 (:parent #54))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("And install with\n" 0 17 (:parent #55))) (src-block (:standard-properties [5321 5321 nil nil 5491 1 nil nil nil nil nil nil nil nil # nil nil #47] :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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #57))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #58))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #59))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #47] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #61))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #47] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #63)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #63] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #63))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #64)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #38]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("GNU Guix allows for " 0 20 (:parent #44)) (link (:standard-properties [6584 nil 6653 6676 6679 1 nil nil nil nil nil nil nil nil # nil nil #44] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #48))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #44))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #41] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #46)) (link (:standard-properties [7007 nil 7112 7122 7124 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #50))) #(".\n" 0 2 (:parent #46))) (paragraph (:standard-properties [7127 7127 7127 7190 7191 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #47))) (fixed-width (:standard-properties [7191 7191 nil nil 7247 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [7247 7247 7247 7250 7251 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("So\n" 0 3 (:parent #49))) (paragraph (:standard-properties [7251 7251 7251 7637 7638 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("#+begin" 0 7 (:parent #50)) (subscript (:standard-properties [7258 nil 7259 7262 7263 1 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("src" 0 3 (:parent #54))) #("sh :lang bash\n#+begin" 0 23 (:parent #50)) (subscript (:standard-properties [7286 nil 7287 7290 7291 1 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("src" 0 3 (:parent #56))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #50)) (subscript (:standard-properties [7331 nil 7332 7339 7339 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #58))) (subscript (:standard-properties [7339 nil 7340 7344 7344 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PATH" 0 4 (:parent #59))) #("=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork\ngenenetwork1 1.0-d622c803b out ../guix-bioinformatics/gn/packages/bioinformatics.scm:163:2\ngenenetwork2 2.0-9e9475053 out ../guix-bioinformatics/gn/packages/bioinformatics.scm:215:2\n#+end" 0 272 (:parent #50)) (subscript (:standard-properties [7616 nil 7617 7620 7621 1 nil nil nil nil nil nil nil nil # 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Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #46))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Once you have succeeded, you have to " 0 37 (:parent #47)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #51))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #47))) (src-block (:standard-properties [2688 2688 nil nil 2796 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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Which should show something like\n" 0 33 (:parent #49))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #43] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) 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The actual installation command of 'hello' is\n" 0 70 (:parent #52))) (src-block (:standard-properties [3022 3022 nil nil 3094 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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #54))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("If you need more help we have another writeup in " 0 49 (:parent #55)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #59))) #(". To get\nrid of the locale warning see " 0 39 (:parent #55)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #61))) #(".\n" 0 2 (:parent #55))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #36] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #41]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. 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The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #57))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #58))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #46] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #60))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #46] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #62)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #62] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #62))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #63)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #37]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("GNU Guix allows for " 0 20 (:parent #43)) (link (:standard-properties [6584 nil 6653 6676 6679 1 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 bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #47))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #43))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #40] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # 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These settings may\nnot reflect your system. To override settings create your own from a copy of\ndefault" 0 105 (:parent #54)) (subscript (:standard-properties [9068 nil 9069 9080 9081 1 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("settings.py" 0 11 (:parent #62))) #("and pass it into GN2 with\n" 0 26 (:parent #54))) (fixed-width (:standard-properties [9108 9108 nil nil 9151 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "./bin/genenetwork2 $HOME/my_settings.py")) (paragraph (:standard-properties [9151 9151 9151 9296 9297 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("and everything " 0 15 (:parent #56)) (bold (:standard-properties [9166 nil 9167 9173 9175 1 nil nil nil nil nil nil nil nil # nil nil #56]) #("should" 0 6 (:parent #60))) #("work (note the full path to the settings\nfile). 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In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #36)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #40))) #("and the main " 0 13 (:parent #36)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #36] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #36))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #25] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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 [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (: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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #34]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #37]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #40))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. If you use a virtual machine we recommend to use at least\ndouble.\n" 0 141 (:parent #41))))) (headline (:standard-properties [1928 1928 1957 3555 3555 0 (:title) nil nil nil nil 1959 3553 2 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 27) t] :title (#("Step 1: Install GNU Guix" 0 24 (: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 [1957 1957 1957 3555 3555 0 nil section nil nil nil 1957 3555 nil # nil nil #35]) (paragraph (:standard-properties [1957 1957 1957 2409 2410 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Fetch the GNU Guix binary from " 0 31 (:parent #41)) (link (:standard-properties [1988 nil 2035 2039 2042 1 nil nil nil nil nil nil nil nil # nil nil #41] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/download/" :format bracket :raw-link "https://www.gnu.org/software/guix/download/" :application nil :search-option nil) #("here" 0 4 (:parent #45))) #("(middle panel) and follow\n" 0 26 (:parent #41)) (link (:standard-properties [2068 nil 2147 2159 2161 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :format bracket :raw-link "https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :application nil :search-option nil) #("instructions" 0 12 (:parent #47))) #(". Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #41))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Once you have succeeded, you have to " 0 37 (:parent #42)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #46))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #42))) (src-block (:standard-properties [2688 2688 nil nil 2796 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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Which should show something like\n" 0 33 (:parent #44))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #38] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) (paragraph (:standard-properties [2940 2940 2940 2950 2951 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("#+end" 0 5 (:parent #46)) (subscript (:standard-properties [2945 nil 2946 2949 2949 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("src" 0 3 (:parent #50))) #("\n" 0 1 (:parent #46))) (paragraph (:standard-properties [2951 2951 2951 3021 3022 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("means binary installs. The actual installation command of 'hello' is\n" 0 70 (:parent #47))) (src-block (:standard-properties [3022 3022 nil nil 3094 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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #49))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("If you need more help we have another writeup in " 0 49 (:parent #50)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #54))) #(". To get\nrid of the locale warning see " 0 39 (:parent #50)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #56))) #(".\n" 0 2 (:parent #50))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #36]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #42))) (src-block (:standard-properties [3721 3721 nil nil 3826 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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #44))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("#+begin" 0 7 (:parent #45)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("src" 0 3 (:parent #49))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #45)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #45)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #45)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("src" 0 3 (:parent #55))) #("bash\n" 0 5 (:parent #45))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("To test whether this is working try:\n" 0 37 (:parent #46))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("#+begin" 0 7 (:parent #47)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("src" 0 3 (:parent #51))) #("bash\n#+end" 0 10 (:parent #47)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("src" 0 3 (:parent #53))) #("bash\n" 0 5 (:parent #47))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #37]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #43))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #40] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("by pasting it into the command\n" 0 31 (:parent #45))) (src-block (:standard-properties [4526 4526 nil nil 4579 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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("and hit Ctrl-D.\n" 0 16 (:parent #47))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #48))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 0 27 (: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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #38]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #44))) (src-block (:standard-properties [4832 4832 nil nil 4951 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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #46))) (src-block (:standard-properties [5004 5004 nil nil 5194 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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #48)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #48]) #("root" 0 4 (:parent #52))) #(".config/guix/latest override).\n" 0 31 (:parent #48))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("And install with\n" 0 17 (:parent #49))) (src-block (:standard-properties [5321 5321 nil nil 5491 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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #51))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #52))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #53))) (src-block (:standard-properties [5961 5961 nil nil 6140 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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #55))) (src-block (:standard-properties [6209 6209 nil nil 6250 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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #57)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #57] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #57))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #58)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #32]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("GNU Guix allows for " 0 20 (:parent #38)) (link (:standard-properties [6584 nil 6653 6676 6679 1 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 bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #42))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #38))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #35] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #40)) (link (:standard-properties [7007 nil 7112 7122 7124 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/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #44))) #(".\n" 0 2 (:parent #40))) (paragraph (:standard-properties [7127 7127 7127 7190 7191 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #41))) (fixed-width (:standard-properties [7191 7191 nil nil 7247 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [7247 7247 7247 7250 7251 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("So\n" 0 3 (:parent #43))) (paragraph (:standard-properties [7251 7251 7251 7637 7638 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("#+begin" 0 7 (:parent #44)) (subscript (:standard-properties [7258 nil 7259 7262 7263 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("src" 0 3 (:parent #48))) #("sh :lang bash\n#+begin" 0 23 (:parent #44)) (subscript (:standard-properties [7286 nil 7287 7290 7291 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("src" 0 3 (:parent #50))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #44)) (subscript (:standard-properties [7331 nil 7332 7339 7339 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #52))) (subscript (:standard-properties [7339 nil 7340 7344 7344 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("PATH" 0 4 (:parent #53))) #("=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork\ngenenetwork1 1.0-d622c803b out ../guix-bioinformatics/gn/packages/bioinformatics.scm:163:2\ngenenetwork2 2.0-9e9475053 out ../guix-bioinformatics/gn/packages/bioinformatics.scm:215:2\n#+end" 0 272 (:parent #44)) (subscript (:standard-properties [7616 nil 7617 7620 7621 1 nil nil nil nil nil nil nil nil # 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For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #359))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. If you use a virtual machine we recommend to use at least\ndouble.\n" 0 141 (:parent #360))))) (headline (:standard-properties [1928 1928 1957 3555 3555 0 (:title) nil nil nil nil 1959 3553 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 27) t] :title (#("Step 1: Install GNU Guix" 0 24 (:parent #354))) :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 [1957 1957 1957 3555 3555 0 nil section nil nil nil 1957 3555 nil # nil nil #354]) (paragraph (:standard-properties [1957 1957 1957 2409 2410 1 nil planning nil nil nil nil nil nil # nil nil #357]) #("Fetch the GNU Guix binary from " 0 31 (:parent #360)) (link (:standard-properties [1988 nil 2035 2039 2042 1 nil nil nil nil nil nil nil nil # nil nil #360] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/download/" :format bracket :raw-link "https://www.gnu.org/software/guix/download/" :application nil :search-option nil) #("here" 0 4 (:parent #364))) #("(middle panel) and follow\n" 0 26 (:parent #360)) (link (:standard-properties [2068 nil 2147 2159 2161 0 nil nil nil nil nil nil nil nil # nil nil #360] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :format bracket :raw-link "https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :application nil :search-option nil) #("instructions" 0 12 (:parent #366))) #(". Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #360))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("Once you have succeeded, you have to " 0 37 (:parent #361)) (link (:standard-properties [2447 nil 2523 2534 2537 1 nil nil nil nil nil nil nil nil # nil nil #361] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #365))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #361))) (src-block (:standard-properties [2688 2688 nil nil 2796 1 nil nil nil nil nil nil nil nil # nil nil #357] :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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("Which should show something like\n" 0 33 (:parent #363))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #357] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) (paragraph (:standard-properties [2940 2940 2940 2950 2951 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("#+end" 0 5 (:parent #365)) (subscript (:standard-properties [2945 nil 2946 2949 2949 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("src" 0 3 (:parent #369))) #("\n" 0 1 (:parent #365))) (paragraph (:standard-properties [2951 2951 2951 3021 3022 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("means binary installs. The actual installation command of 'hello' is\n" 0 70 (:parent #366))) (src-block (:standard-properties [3022 3022 nil nil 3094 1 nil nil nil nil nil nil nil nil # nil nil #357] :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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #368))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("If you need more help we have another writeup in " 0 49 (:parent #369)) (link (:standard-properties [3330 nil 3414 3424 3426 0 nil nil nil nil nil nil nil nil # nil nil #369] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #373))) #(". To get\nrid of the locale warning see " 0 39 (:parent #369)) (link (:standard-properties [3465 nil 3540 3550 3552 0 nil nil nil nil nil nil nil nil # nil nil #369] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #375))) #(".\n" 0 2 (:parent #369))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (:parent #355))) :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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #355]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #361))) (src-block (:standard-properties [3721 3721 nil nil 3826 1 nil nil nil nil nil nil nil nil # nil nil #358] :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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #363))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("#+begin" 0 7 (:parent #364)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #364] :use-brackets-p nil) #("src" 0 3 (:parent #368))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #364)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #364] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #364)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #364] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #364)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #364] :use-brackets-p nil) #("src" 0 3 (:parent #374))) #("bash\n" 0 5 (:parent #364))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("To test whether this is working try:\n" 0 37 (:parent #365))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("#+begin" 0 7 (:parent #366)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("src" 0 3 (:parent #370))) #("bash\n#+end" 0 10 (:parent #366)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("src" 0 3 (:parent #372))) #("bash\n" 0 5 (:parent #366))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #356]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #359]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #362))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #359] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("by pasting it into the command\n" 0 31 (:parent #364))) (src-block (:standard-properties [4526 4526 nil nil 4579 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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("and hit Ctrl-D.\n" 0 16 (:parent #366))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #367))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 0 27 (: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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #357]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #360]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #363))) (src-block (:standard-properties [4832 4832 nil nil 4951 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #365))) (src-block (:standard-properties [5004 5004 nil nil 5194 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #367)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #367]) #("root" 0 4 (:parent #371))) #(".config/guix/latest override).\n" 0 31 (:parent #367))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("And install with\n" 0 17 (:parent #368))) (src-block (:standard-properties [5321 5321 nil nil 5491 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #370))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #371))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #372))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #374))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #376)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #376] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #376))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #377)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #351]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #354]) #("GNU Guix allows for " 0 20 (:parent #357)) (link (:standard-properties [6584 nil 6653 6676 6679 1 nil nil nil nil nil nil nil nil # nil nil #357] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #361))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #357))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #354] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #359)) (link (:standard-properties [7007 nil 7112 7122 7124 0 nil nil nil nil nil nil nil nil # nil nil #359] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #363))) #(".\n" 0 2 (:parent #359))) (paragraph (:standard-properties [7127 7127 7127 7190 7191 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #360))) (fixed-width (:standard-properties [7191 7191 nil nil 7247 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [7247 7247 7247 7250 7251 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("So\n" 0 3 (:parent #362))) (paragraph (:standard-properties [7251 7251 7251 7637 7638 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("#+begin" 0 7 (:parent #363)) (subscript (:standard-properties [7258 nil 7259 7262 7263 1 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("src" 0 3 (:parent #367))) #("sh :lang bash\n#+begin" 0 23 (:parent #363)) (subscript (:standard-properties [7286 nil 7287 7290 7291 1 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("src" 0 3 (:parent #369))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #363)) (subscript (:standard-properties [7331 nil 7332 7339 7339 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #371))) (subscript (:standard-properties [7339 nil 7340 7344 7344 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("PATH" 0 4 (:parent #372))) #("=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork\ngenenetwork1 1.0-d622c803b out ../guix-bioinformatics/gn/packages/bioinformatics.scm:163:2\ngenenetwork2 2.0-9e9475053 out ../guix-bioinformatics/gn/packages/bioinformatics.scm:215:2\n#+end" 0 272 (:parent #363)) (subscript (:standard-properties [7616 nil 7617 7620 7621 1 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("src" 0 3 (:parent #374))) #("sh :lang bash\n" 0 16 (:parent #363))) (paragraph (:standard-properties [7638 7638 7638 7651 7652 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("Install with\n" 0 13 (:parent #364))) (paragraph (:standard-properties [7652 7652 7652 7811 7812 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("#+begin" 0 7 (:parent #365)) (subscript (:standard-properties [7659 nil 7660 7663 7664 1 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("src" 0 3 (:parent #369))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #365)) (subscript (:standard-properties [7704 nil 7705 7712 7712 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #371))) (subscript (:standard-properties [7712 nil 7713 7717 7717 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("PATH" 0 4 (:parent #372))) #("=../guix-bioinformatics ./pre-inst-env guix package -i genenetwork2\n#+end" 0 73 (:parent #365)) (subscript (:standard-properties [7790 nil 7791 7794 7795 1 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("src" 0 3 (:parent #374))) #("sh :lang bash\n" 0 16 (:parent #365))))) (headline (:standard-properties [7812 7812 7830 7977 7977 0 (:title) nil nil nil nil 7832 7975 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 16) t] :title (#("Create archive" 0 14 (: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 [7830 7830 7830 7977 7977 0 nil section nil nil nil 7830 7977 nil # nil nil #352]) (fixed-width (:standard-properties [7830 7830 nil nil 7977 3 nil planning nil nil nil nil nil nil # nil nil #355] :value "env GUIX_PACKAGE_PATH=../../genenetwork/guix-bioinformatics/ ./pre-inst-env guix archive --export -r genenetwork2 > guix_gn2-2.0-9e9475053.nar")))) (headline (:standard-properties [7977 7977 7998 11645 11645 0 (:title) nil nil nil nil 8000 11643 1 # 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nil nil #28] :key "TITLE" :value "Installing GeneNetwork services with GNU Guix"))) #20 (headline (:standard-properties [1130 1130 1146 1409 1409 0 (:title) nil nil nil nil 1148 1407 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 [1146 1146 1146 1409 1409 0 nil section nil nil nil 1146 1409 nil # nil nil #30]) (paragraph (:standard-properties [1146 1146 1146 1408 1409 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("Large system deployments tend to get very complex. In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #36)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #40))) #("and the main " 0 13 (:parent #36)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #36] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #36))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #25] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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 [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (: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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #34]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #37]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #40))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. 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Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #41))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Once you have succeeded, you have to " 0 37 (:parent #42)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #46))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #42))) (src-block (:standard-properties [2688 2688 nil nil 2796 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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Which should show something like\n" 0 33 (:parent #44))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #38] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) 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The actual installation command of 'hello' is\n" 0 70 (:parent #47))) (src-block (:standard-properties [3022 3022 nil nil 3094 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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #49))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("If you need more help we have another writeup in " 0 49 (:parent #50)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #54))) #(". To get\nrid of the locale warning see " 0 39 (:parent #50)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #56))) #(".\n" 0 2 (:parent #50))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #36]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #42))) (src-block (:standard-properties [3721 3721 nil nil 3826 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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #44))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("#+begin" 0 7 (:parent #45)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("src" 0 3 (:parent #49))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #45)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #45)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #45)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("src" 0 3 (:parent #55))) #("bash\n" 0 5 (:parent #45))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("To test whether this is working try:\n" 0 37 (:parent #46))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("#+begin" 0 7 (:parent #47)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("src" 0 3 (:parent #51))) #("bash\n#+end" 0 10 (:parent #47)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("src" 0 3 (:parent #53))) #("bash\n" 0 5 (:parent #47))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #37]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("GN2 has its own GNU Guix binary distribution server. 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The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #52))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #53))) (src-block (:standard-properties [5961 5961 nil nil 6140 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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #55))) (src-block (:standard-properties [6209 6209 nil nil 6250 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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. 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These settings may\nnot reflect your system. To override settings create your own from a copy of\ndefault" 0 105 (:parent #49)) (subscript (:standard-properties [9068 nil 9069 9080 9081 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("settings.py" 0 11 (:parent #57))) #("and pass it into GN2 with\n" 0 26 (:parent #49))) (fixed-width (:standard-properties [9108 9108 nil nil 9151 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "./bin/genenetwork2 $HOME/my_settings.py")) (paragraph (:standard-properties [9151 9151 9151 9296 9297 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("and everything " 0 15 (:parent #51)) (bold (:standard-properties [9166 nil 9167 9173 9175 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("should" 0 6 (:parent #55))) #("work (note the full path to the settings\nfile). 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In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #37)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #41))) #("and the main " 0 13 (:parent #37)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #37] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #37))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #26] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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 [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (: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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #35]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #38]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #41))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. If you use a virtual machine we recommend to use at least\ndouble.\n" 0 141 (:parent #42))))) (headline (:standard-properties [1928 1928 1957 3555 3555 0 (:title) nil nil nil nil 1959 3553 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 27) t] :title (#("Step 1: Install GNU Guix" 0 24 (: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 [1957 1957 1957 3555 3555 0 nil section nil nil nil 1957 3555 nil # nil nil #36]) (paragraph (:standard-properties [1957 1957 1957 2409 2410 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("Fetch the GNU Guix binary from " 0 31 (:parent #42)) (link (:standard-properties [1988 nil 2035 2039 2042 1 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/download/" :format bracket :raw-link "https://www.gnu.org/software/guix/download/" :application nil :search-option nil) #("here" 0 4 (:parent #46))) #("(middle panel) and follow\n" 0 26 (:parent #42)) (link (:standard-properties [2068 nil 2147 2159 2161 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :format bracket :raw-link "https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :application nil :search-option nil) #("instructions" 0 12 (:parent #48))) #(". Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #42))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Once you have succeeded, you have to " 0 37 (:parent #43)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #47))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #43))) (src-block (:standard-properties [2688 2688 nil nil 2796 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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Which should show something like\n" 0 33 (:parent #45))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #39] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) (paragraph (:standard-properties [2940 2940 2940 2950 2951 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("#+end" 0 5 (:parent #47)) (subscript (:standard-properties [2945 nil 2946 2949 2949 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("src" 0 3 (:parent #51))) #("\n" 0 1 (:parent #47))) (paragraph (:standard-properties [2951 2951 2951 3021 3022 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("means binary installs. The actual installation command of 'hello' is\n" 0 70 (:parent #48))) (src-block (:standard-properties [3022 3022 nil nil 3094 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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #50))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("If you need more help we have another writeup in " 0 49 (:parent #51)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #55))) #(". To get\nrid of the locale warning see " 0 39 (:parent #51)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #57))) #(".\n" 0 2 (:parent #51))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #37]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #43))) (src-block (:standard-properties [3721 3721 nil nil 3826 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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #45))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("#+begin" 0 7 (:parent #46)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("src" 0 3 (:parent #50))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #46)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #46)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #46)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("src" 0 3 (:parent #56))) #("bash\n" 0 5 (:parent #46))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("To test whether this is working try:\n" 0 37 (:parent #47))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("#+begin" 0 7 (:parent #48)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("src" 0 3 (:parent #52))) #("bash\n#+end" 0 10 (:parent #48)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("src" 0 3 (:parent #54))) #("bash\n" 0 5 (:parent #48))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #38]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #44))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #41] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("by pasting it into the command\n" 0 31 (:parent #46))) (src-block (:standard-properties [4526 4526 nil nil 4579 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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("and hit Ctrl-D.\n" 0 16 (:parent #48))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #49))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #39]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #45))) (src-block (:standard-properties [4832 4832 nil nil 4951 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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #47))) (src-block (:standard-properties [5004 5004 nil nil 5194 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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #49)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #49]) #("root" 0 4 (:parent #53))) #(".config/guix/latest override).\n" 0 31 (:parent #49))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("And install with\n" 0 17 (:parent #50))) (src-block (:standard-properties [5321 5321 nil nil 5491 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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #52))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #53))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #54))) (src-block (:standard-properties [5961 5961 nil nil 6140 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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #56))) (src-block (:standard-properties [6209 6209 nil nil 6250 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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #58)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #58] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #58))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #59)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #33]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("GNU Guix allows for " 0 20 (:parent #39)) (link (:standard-properties [6584 nil 6653 6676 6679 1 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/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #43))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #39))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #36] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #41)) (link (:standard-properties [7007 nil 7112 7122 7124 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/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #45))) #(".\n" 0 2 (:parent #41))) (paragraph (:standard-properties [7127 7127 7127 7190 7191 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #42))) (fixed-width (:standard-properties [7191 7191 nil nil 7247 2 nil nil nil nil nil nil nil nil # nil nil #36] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [7247 7247 7247 7250 7251 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("So\n" 0 3 (:parent #44))) (paragraph (:standard-properties [7251 7251 7251 7637 7638 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("#+begin" 0 7 (:parent #45)) (subscript (:standard-properties [7258 nil 7259 7262 7263 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("src" 0 3 (:parent #49))) #("sh :lang bash\n#+begin" 0 23 (:parent #45)) (subscript (:standard-properties [7286 nil 7287 7290 7291 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("src" 0 3 (:parent #51))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #45)) (subscript (:standard-properties [7331 nil 7332 7339 7339 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #53))) (subscript (:standard-properties [7339 nil 7340 7344 7344 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("PATH" 0 4 (:parent #54))) #("=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork\ngenenetwork1 1.0-d622c803b out ../guix-bioinformatics/gn/packages/bioinformatics.scm:163:2\ngenenetwork2 2.0-9e9475053 out ../guix-bioinformatics/gn/packages/bioinformatics.scm:215:2\n#+end" 0 272 (:parent #45)) (subscript (:standard-properties [7616 nil 7617 7620 7621 1 nil nil nil nil nil nil nil nil # 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Press Ctrl-C to interrupt.\n" 0 186 (:parent #44))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("If you need more help we have another writeup in " 0 49 (:parent #45)) (link (:standard-properties [3330 nil 3414 3424 3426 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #49))) #(". To get\nrid of the locale warning see " 0 39 (:parent #45)) (link (:standard-properties [3465 nil 3540 3550 3552 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #51))) #(".\n" 0 2 (:parent #45))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #31]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. 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The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #47))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #48))) (src-block (:standard-properties [5961 5961 nil nil 6140 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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #50))) (src-block (:standard-properties [6209 6209 nil nil 6250 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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. 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Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #360))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("Once you have succeeded, you have to " 0 37 (:parent #361)) (link (:standard-properties [2447 nil 2523 2534 2537 1 nil nil nil nil nil nil nil nil # nil nil #361] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #365))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #361))) (src-block (:standard-properties [2688 2688 nil nil 2796 1 nil nil nil nil nil nil nil nil # nil nil #357] :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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("Which should show something like\n" 0 33 (:parent #363))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #357] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) 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The actual installation command of 'hello' is\n" 0 70 (:parent #366))) (src-block (:standard-properties [3022 3022 nil nil 3094 1 nil nil nil nil nil nil nil nil # nil nil #357] :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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #368))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("If you need more help we have another writeup in " 0 49 (:parent #369)) (link (:standard-properties [3330 nil 3414 3424 3426 0 nil nil nil nil nil nil nil nil # nil nil #369] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #373))) #(". To get\nrid of the locale warning see " 0 39 (:parent #369)) (link (:standard-properties [3465 nil 3540 3550 3552 0 nil nil nil nil nil nil nil nil # nil nil #369] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #375))) #(".\n" 0 2 (:parent #369))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (:parent #355))) :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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #355]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #361))) (src-block (:standard-properties [3721 3721 nil nil 3826 1 nil nil nil nil nil nil nil nil # nil nil #358] :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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #363))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("#+begin" 0 7 (:parent #364)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #364] :use-brackets-p nil) #("src" 0 3 (:parent #368))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #364)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #364] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #364)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #364] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #364)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #364] :use-brackets-p nil) #("src" 0 3 (:parent #374))) #("bash\n" 0 5 (:parent #364))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("To test whether this is working try:\n" 0 37 (:parent #365))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("#+begin" 0 7 (:parent #366)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("src" 0 3 (:parent #370))) #("bash\n#+end" 0 10 (:parent #366)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("src" 0 3 (:parent #372))) #("bash\n" 0 5 (:parent #366))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #356]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #359]) #("GN2 has its own GNU Guix binary distribution server. 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The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #371))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #372))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #374))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #376)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #376] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #376))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #377)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #351]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #354]) #("GNU Guix allows for " 0 20 (:parent #357)) (link (:standard-properties [6584 nil 6653 6676 6679 1 nil nil nil nil nil nil nil nil # nil nil #357] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #361))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #357))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #354] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # 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nil nil #23] :key "TITLE" :value "Installing GeneNetwork services with GNU Guix"))) #15 (headline (:standard-properties [1130 1130 1146 1409 1409 0 (:title) nil nil nil nil 1148 1407 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 [1146 1146 1146 1409 1409 0 nil section nil nil nil 1146 1409 nil # nil nil #25]) (paragraph (:standard-properties [1146 1146 1146 1408 1409 1 nil planning nil nil nil nil nil nil # nil nil #28]) #("Large system deployments tend to get very complex. In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #31)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #35))) #("and the main " 0 13 (:parent #31)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #31] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #31))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #20] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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) (headline (:standard-properties [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (: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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #29]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #32]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #35))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. 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Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #36))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("Once you have succeeded, you have to " 0 37 (:parent #37)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #41))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #37))) (src-block (:standard-properties [2688 2688 nil nil 2796 1 nil nil nil nil nil nil nil nil # nil nil #33] :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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("Which should show something like\n" 0 33 (:parent #39))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #33] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) (paragraph (:standard-properties [2940 2940 2940 2950 2951 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("#+end" 0 5 (:parent #41)) (subscript (:standard-properties [2945 nil 2946 2949 2949 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("src" 0 3 (:parent #45))) #("\n" 0 1 (:parent #41))) (paragraph (:standard-properties [2951 2951 2951 3021 3022 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("means binary installs. The actual installation command of 'hello' is\n" 0 70 (:parent #42))) (src-block (:standard-properties [3022 3022 nil nil 3094 1 nil nil nil nil nil nil nil nil # nil nil #33] :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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #44))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("If you need more help we have another writeup in " 0 49 (:parent #45)) (link (:standard-properties [3330 nil 3414 3424 3426 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #49))) #(". To get\nrid of the locale warning see " 0 39 (:parent #45)) (link (:standard-properties [3465 nil 3540 3550 3552 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #51))) #(".\n" 0 2 (:parent #45))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #31]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #37))) (src-block (:standard-properties [3721 3721 nil nil 3826 1 nil nil nil nil nil nil nil nil # nil nil #34] :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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #39))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("#+begin" 0 7 (:parent #40)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("src" 0 3 (:parent #44))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #40)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #40] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #40)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #40] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #40)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("src" 0 3 (:parent #50))) #("bash\n" 0 5 (:parent #40))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("To test whether this is working try:\n" 0 37 (:parent #41))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("#+begin" 0 7 (:parent #42)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("src" 0 3 (:parent #46))) #("bash\n#+end" 0 10 (:parent #42)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("src" 0 3 (:parent #48))) #("bash\n" 0 5 (:parent #42))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #32]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #38))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #35] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("by pasting it into the command\n" 0 31 (:parent #40))) (src-block (:standard-properties [4526 4526 nil nil 4579 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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("and hit Ctrl-D.\n" 0 16 (:parent #42))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #43))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 0 27 (: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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #33]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #39))) (src-block (:standard-properties [4832 4832 nil nil 4951 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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #41))) (src-block (:standard-properties [5004 5004 nil nil 5194 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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #43)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #43]) #("root" 0 4 (:parent #47))) #(".config/guix/latest override).\n" 0 31 (:parent #43))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("And install with\n" 0 17 (:parent #44))) (src-block (:standard-properties [5321 5321 nil nil 5491 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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #46))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #47))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #48))) (src-block (:standard-properties [5961 5961 nil nil 6140 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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #50))) (src-block (:standard-properties [6209 6209 nil nil 6250 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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #52)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #52))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #53)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #27]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #30]) #("GNU Guix allows for " 0 20 (:parent #33)) (link (:standard-properties [6584 nil 6653 6676 6679 1 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/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #37))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #33))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #30] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #35)) (link (:standard-properties [7007 nil 7112 7122 7124 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/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #39))) #(".\n" 0 2 (:parent #35))) (paragraph (:standard-properties [7127 7127 7127 7190 7191 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #36))) (fixed-width (:standard-properties [7191 7191 nil nil 7247 2 nil nil nil nil nil nil nil nil # nil nil #30] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [7247 7247 7247 7250 7251 1 nil nil nil nil nil nil nil nil # 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Press Ctrl-C to interrupt.\n" 0 186 (:parent #45))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("If you need more help we have another writeup in " 0 49 (:parent #46)) (link (:standard-properties [3330 nil 3414 3424 3426 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #50))) #(". To get\nrid of the locale warning see " 0 39 (:parent #46)) (link (:standard-properties [3465 nil 3540 3550 3552 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #52))) #(".\n" 0 2 (:parent #46))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #32]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. 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The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #48))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #49))) (src-block (:standard-properties [5961 5961 nil nil 6140 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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #51))) (src-block (:standard-properties [6209 6209 nil nil 6250 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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. 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nil nil (headline (:standard-properties [57 57 135 1130 1130 0 (:title) nil nil nil nil 137 1128 1 # nil nil (org-data (:standard-properties [1 1 1 13393 13393 0 nil org-data nil nil nil 3 13393 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 57 57 0 nil first-section nil nil nil 1 57 nil # nil nil #22]) (keyword (:standard-properties [1 1 nil nil 57 1 nil top-comment nil nil nil nil nil nil # nil nil #25] :key "TITLE" :value "Installing GeneNetwork services with GNU Guix"))) #17 (headline (:standard-properties [1130 1130 1146 1409 1409 0 (:title) nil nil nil nil 1148 1407 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 [1146 1146 1146 1409 1409 0 nil section nil nil nil 1146 1409 nil # nil nil #27]) (paragraph (:standard-properties [1146 1146 1146 1408 1409 1 nil planning nil nil nil nil nil nil # nil nil #30]) #("Large system deployments tend to get very complex. In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #33)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #37))) #("and the main " 0 13 (:parent #33)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #33] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #33))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #22] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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 [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (: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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #31]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #34]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #37))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. 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Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #38))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("Once you have succeeded, you have to " 0 37 (:parent #39)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #43))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #39))) (src-block (:standard-properties [2688 2688 nil nil 2796 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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("Which should show something like\n" 0 33 (:parent #41))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #35] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) (paragraph (:standard-properties [2940 2940 2940 2950 2951 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("#+end" 0 5 (:parent #43)) (subscript (:standard-properties [2945 nil 2946 2949 2949 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("src" 0 3 (:parent #47))) #("\n" 0 1 (:parent #43))) (paragraph (:standard-properties [2951 2951 2951 3021 3022 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("means binary installs. The actual installation command of 'hello' is\n" 0 70 (:parent #44))) (src-block (:standard-properties [3022 3022 nil nil 3094 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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #46))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("If you need more help we have another writeup in " 0 49 (:parent #47)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #51))) #(". To get\nrid of the locale warning see " 0 39 (:parent #47)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #53))) #(".\n" 0 2 (:parent #47))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #33]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #39))) (src-block (:standard-properties [3721 3721 nil nil 3826 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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #41))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("#+begin" 0 7 (:parent #42)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("src" 0 3 (:parent #46))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #42)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #42)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #42)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("src" 0 3 (:parent #52))) #("bash\n" 0 5 (:parent #42))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("To test whether this is working try:\n" 0 37 (:parent #43))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("#+begin" 0 7 (:parent #44)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("src" 0 3 (:parent #48))) #("bash\n#+end" 0 10 (:parent #44)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("src" 0 3 (:parent #50))) #("bash\n" 0 5 (:parent #44))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #34]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #40))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #37] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("by pasting it into the command\n" 0 31 (:parent #42))) (src-block (:standard-properties [4526 4526 nil nil 4579 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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("and hit Ctrl-D.\n" 0 16 (:parent #44))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #45))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #35]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #41))) (src-block (:standard-properties [4832 4832 nil nil 4951 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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #43))) (src-block (:standard-properties [5004 5004 nil nil 5194 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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #45)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #45]) #("root" 0 4 (:parent #49))) #(".config/guix/latest override).\n" 0 31 (:parent #45))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("And install with\n" 0 17 (:parent #46))) (src-block (:standard-properties [5321 5321 nil nil 5491 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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #48))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #49))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #50))) (src-block (:standard-properties [5961 5961 nil nil 6140 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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #52))) (src-block (:standard-properties [6209 6209 nil nil 6250 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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #54)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #54] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #54))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #55)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #29]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #32]) #("GNU Guix allows for " 0 20 (:parent #35)) (link (:standard-properties [6584 nil 6653 6676 6679 1 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/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #39))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #35))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #32] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #37)) (link (:standard-properties [7007 nil 7112 7122 7124 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/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #41))) #(".\n" 0 2 (:parent #37))) (paragraph (:standard-properties [7127 7127 7127 7190 7191 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #38))) (fixed-width (:standard-properties [7191 7191 nil nil 7247 2 nil nil nil nil nil nil nil nil # nil nil #32] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [7247 7247 7247 7250 7251 1 nil nil nil nil nil nil nil nil # 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In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #34)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #38))) #("and the main " 0 13 (:parent #34)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #34] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #34))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #23] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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 [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (: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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #32]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #35]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #38))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. If you use a virtual machine we recommend to use at least\ndouble.\n" 0 141 (:parent #39))))) (headline (:standard-properties [1928 1928 1957 3555 3555 0 (:title) nil nil nil nil 1959 3553 2 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 27) t] :title (#("Step 1: Install GNU Guix" 0 24 (: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 [1957 1957 1957 3555 3555 0 nil section nil nil nil 1957 3555 nil # nil nil #33]) (paragraph (:standard-properties [1957 1957 1957 2409 2410 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("Fetch the GNU Guix binary from " 0 31 (:parent #39)) (link (:standard-properties [1988 nil 2035 2039 2042 1 nil nil nil nil nil nil nil nil # nil nil #39] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/download/" :format bracket :raw-link "https://www.gnu.org/software/guix/download/" :application nil :search-option nil) #("here" 0 4 (:parent #43))) #("(middle panel) and follow\n" 0 26 (:parent #39)) (link (:standard-properties [2068 nil 2147 2159 2161 0 nil nil nil nil nil nil nil nil # nil nil #39] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :format bracket :raw-link "https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :application nil :search-option nil) #("instructions" 0 12 (:parent #45))) #(". Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #39))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("Once you have succeeded, you have to " 0 37 (:parent #40)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #44))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #40))) (src-block (:standard-properties [2688 2688 nil nil 2796 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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("Which should show something like\n" 0 33 (:parent #42))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #36] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) (paragraph (:standard-properties [2940 2940 2940 2950 2951 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("#+end" 0 5 (:parent #44)) (subscript (:standard-properties [2945 nil 2946 2949 2949 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("src" 0 3 (:parent #48))) #("\n" 0 1 (:parent #44))) (paragraph (:standard-properties [2951 2951 2951 3021 3022 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("means binary installs. The actual installation command of 'hello' is\n" 0 70 (:parent #45))) (src-block (:standard-properties [3022 3022 nil nil 3094 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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #47))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("If you need more help we have another writeup in " 0 49 (:parent #48)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #52))) #(". To get\nrid of the locale warning see " 0 39 (:parent #48)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #54))) #(".\n" 0 2 (:parent #48))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #34]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #40))) (src-block (:standard-properties [3721 3721 nil nil 3826 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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #42))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("#+begin" 0 7 (:parent #43)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("src" 0 3 (:parent #47))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #43)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #43)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #43] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #43)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("src" 0 3 (:parent #53))) #("bash\n" 0 5 (:parent #43))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("To test whether this is working try:\n" 0 37 (:parent #44))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("#+begin" 0 7 (:parent #45)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("src" 0 3 (:parent #49))) #("bash\n#+end" 0 10 (:parent #45)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("src" 0 3 (:parent #51))) #("bash\n" 0 5 (:parent #45))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #35]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #41))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #38] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("by pasting it into the command\n" 0 31 (:parent #43))) (src-block (:standard-properties [4526 4526 nil nil 4579 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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("and hit Ctrl-D.\n" 0 16 (:parent #45))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #46))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 0 27 (: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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #36]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #42))) (src-block (:standard-properties [4832 4832 nil nil 4951 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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #44))) (src-block (:standard-properties [5004 5004 nil nil 5194 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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #46)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #46]) #("root" 0 4 (:parent #50))) #(".config/guix/latest override).\n" 0 31 (:parent #46))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("And install with\n" 0 17 (:parent #47))) (src-block (:standard-properties [5321 5321 nil nil 5491 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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #49))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #50))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #51))) (src-block (:standard-properties [5961 5961 nil nil 6140 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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #53))) (src-block (:standard-properties [6209 6209 nil nil 6250 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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #55)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #55] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #55))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #56)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #30]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("GNU Guix allows for " 0 20 (:parent #36)) (link (:standard-properties [6584 nil 6653 6676 6679 1 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/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #40))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #36))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #33] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #38)) (link (:standard-properties [7007 nil 7112 7122 7124 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/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #42))) #(".\n" 0 2 (:parent #38))) (paragraph (:standard-properties [7127 7127 7127 7190 7191 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #39))) (fixed-width (:standard-properties [7191 7191 nil nil 7247 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [7247 7247 7247 7250 7251 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("So\n" 0 3 (:parent #41))) (paragraph (:standard-properties [7251 7251 7251 7637 7638 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("#+begin" 0 7 (:parent #42)) (subscript (:standard-properties [7258 nil 7259 7262 7263 1 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("src" 0 3 (:parent #46))) #("sh :lang bash\n#+begin" 0 23 (:parent #42)) (subscript (:standard-properties [7286 nil 7287 7290 7291 1 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("src" 0 3 (:parent #48))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #42)) (subscript (:standard-properties [7331 nil 7332 7339 7339 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #50))) (subscript (:standard-properties [7339 nil 7340 7344 7344 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("PATH" 0 4 (:parent #51))) #("=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork\ngenenetwork1 1.0-d622c803b out ../guix-bioinformatics/gn/packages/bioinformatics.scm:163:2\ngenenetwork2 2.0-9e9475053 out ../guix-bioinformatics/gn/packages/bioinformatics.scm:215:2\n#+end" 0 272 (:parent #42)) (subscript (:standard-properties [7616 nil 7617 7620 7621 1 nil nil nil nil nil nil nil nil # 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In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #35)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #39))) #("and the main " 0 13 (:parent #35)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #35] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #35))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #24] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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 [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (: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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #33]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #36]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #39))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. 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Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #40))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("Once you have succeeded, you have to " 0 37 (:parent #41)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #45))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #41))) (src-block (:standard-properties [2688 2688 nil nil 2796 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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("Which should show something like\n" 0 33 (:parent #43))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #37] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) 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Press Ctrl-C to interrupt.\n" 0 186 (:parent #48))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("If you need more help we have another writeup in " 0 49 (:parent #49)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #53))) #(". To get\nrid of the locale warning see " 0 39 (:parent #49)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #55))) #(".\n" 0 2 (:parent #49))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #35]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #41))) (src-block (:standard-properties [3721 3721 nil nil 3826 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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #43))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("#+begin" 0 7 (:parent #44)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("src" 0 3 (:parent #48))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #44)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #44)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #44] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #44)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("src" 0 3 (:parent #54))) #("bash\n" 0 5 (:parent #44))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("To test whether this is working try:\n" 0 37 (:parent #45))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("#+begin" 0 7 (:parent #46)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("src" 0 3 (:parent #50))) #("bash\n#+end" 0 10 (:parent #46)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("src" 0 3 (:parent #52))) #("bash\n" 0 5 (:parent #46))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #36]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("GN2 has its own GNU Guix binary distribution server. 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The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #51))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #52))) (src-block (:standard-properties [5961 5961 nil nil 6140 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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #54))) (src-block (:standard-properties [6209 6209 nil nil 6250 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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #56)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #56] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #56))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #57)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # 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These settings may\nnot reflect your system. To override settings create your own from a copy of\ndefault" 0 105 (:parent #48)) (subscript (:standard-properties [9068 nil 9069 9080 9081 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("settings.py" 0 11 (:parent #56))) #("and pass it into GN2 with\n" 0 26 (:parent #48))) (fixed-width (:standard-properties [9108 9108 nil nil 9151 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "./bin/genenetwork2 $HOME/my_settings.py")) (paragraph (:standard-properties [9151 9151 9151 9296 9297 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("and everything " 0 15 (:parent #50)) (bold (:standard-properties [9166 nil 9167 9173 9175 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("should" 0 6 (:parent #54))) #("work (note the full path to the settings\nfile). 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A configuration file for\nGeneNetwork (reverse proxy) port forwarding can be found in the source\nrepository under ./etc/nginx-genenetwork.conf. Copy this file to /etc\n(still as root)\n" 0 226 (:parent #54))) (fixed-width (:standard-properties [11404 11404 nil nil 11451 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "cp ./etc/nginx-genenetwork.conf /etc/nginx/")) (paragraph (:standard-properties [11451 11451 11451 11461 11462 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Make dirs\n" 0 10 (:parent #56))) (fixed-width (:standard-properties [11462 11462 nil nil 11496 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "mkdir -p /var/spool/nginx/logs")) (paragraph (:standard-properties [11496 11496 11496 11506 11507 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Add users\n" 0 10 (:parent #58))) (fixed-width (:standard-properties [11507 11507 nil nil 11543 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "adduser nobody ; addgroup nobody")) (paragraph (:standard-properties [11543 11543 11543 11553 11554 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Run nginx\n" 0 10 (:parent #60))) (fixed-width (:standard-properties [11554 11554 nil nil 11645 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "/root/.guix-profile/sbin/nginx -c /etc/nginx/nginx-genenetwork.conf -p /var/spool/nginx"))))) (headline (:standard-properties [11645 11645 11707 13393 13393 0 (:title) nil nil nil nil 11709 13391 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 60) t] :title (#("Source deployment and other information on reproducibility" 0 58 (: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 [11707 11707 11707 11764 11764 0 nil section nil nil nil 11707 11764 nil # nil nil #34]) (paragraph (:standard-properties [11707 11707 11707 11763 11764 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("See the document " 0 17 (:parent #40)) (link (:standard-properties [11724 nil nil nil 11761 0 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)) #(".\n" 0 2 (:parent #40)))) (headline (:standard-properties [11764 11764 11790 12214 12214 0 (:title) nil nil nil nil 11792 12212 2 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 24) t] :title (#("Update to recent guix" 0 21 (: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 [11790 11790 11790 12214 12214 0 nil section nil nil nil 11790 12214 nil # nil nil #38]) (paragraph (:standard-properties [11790 11790 11790 11824 11825 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("We now compile Guix from scratch.\n" 0 34 (:parent #44))) (paragraph (:standard-properties [11825 11825 11825 12099 12100 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Create, install and run a recent version of the guix-daemon by\ncompiling the guix repository you have installed with git in\nstep 2. 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nil nil #30]) (paragraph (:standard-properties [1146 1146 1146 1408 1409 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("Large system deployments tend to get very complex. In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #36)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #40))) #("and the main " 0 13 (:parent #36)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #36] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #36))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #25] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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 [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (: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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #34]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #37]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #40))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. 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Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #41))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Once you have succeeded, you have to " 0 37 (:parent #42)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #46))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #42))) (src-block (:standard-properties [2688 2688 nil nil 2796 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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Which should show something like\n" 0 33 (:parent #44))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #38] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) 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The actual installation command of 'hello' is\n" 0 70 (:parent #47))) (src-block (:standard-properties [3022 3022 nil nil 3094 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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #49))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("If you need more help we have another writeup in " 0 49 (:parent #50)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #54))) #(". To get\nrid of the locale warning see " 0 39 (:parent #50)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #56))) #(".\n" 0 2 (:parent #50))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #36]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #42))) (src-block (:standard-properties [3721 3721 nil nil 3826 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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #44))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("#+begin" 0 7 (:parent #45)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("src" 0 3 (:parent #49))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #45)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #45)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #45)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("src" 0 3 (:parent #55))) #("bash\n" 0 5 (:parent #45))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("To test whether this is working try:\n" 0 37 (:parent #46))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("#+begin" 0 7 (:parent #47)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("src" 0 3 (:parent #51))) #("bash\n#+end" 0 10 (:parent #47)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("src" 0 3 (:parent #53))) #("bash\n" 0 5 (:parent #47))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #37]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #43))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #40] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("by pasting it into the command\n" 0 31 (:parent #45))) (src-block (:standard-properties [4526 4526 nil nil 4579 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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("and hit Ctrl-D.\n" 0 16 (:parent #47))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #48))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 0 27 (: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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #38]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #44))) (src-block (:standard-properties [4832 4832 nil nil 4951 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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #46))) (src-block (:standard-properties [5004 5004 nil nil 5194 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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #48)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #48]) #("root" 0 4 (:parent #52))) #(".config/guix/latest override).\n" 0 31 (:parent #48))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("And install with\n" 0 17 (:parent #49))) (src-block (:standard-properties [5321 5321 nil nil 5491 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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #51))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #52))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #53))) (src-block (:standard-properties [5961 5961 nil nil 6140 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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #55))) (src-block (:standard-properties [6209 6209 nil nil 6250 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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #57)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #57] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #57))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #58)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # 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Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #42))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Once you have succeeded, you have to " 0 37 (:parent #43)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #47))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #43))) (src-block (:standard-properties [2688 2688 nil nil 2796 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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Which should show something like\n" 0 33 (:parent #45))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #39] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) (paragraph (:standard-properties [2940 2940 2940 2950 2951 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("#+end" 0 5 (:parent #47)) (subscript (:standard-properties [2945 nil 2946 2949 2949 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("src" 0 3 (:parent #51))) #("\n" 0 1 (:parent #47))) (paragraph (:standard-properties [2951 2951 2951 3021 3022 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("means binary installs. The actual installation command of 'hello' is\n" 0 70 (:parent #48))) (src-block (:standard-properties [3022 3022 nil nil 3094 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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #50))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("If you need more help we have another writeup in " 0 49 (:parent #51)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #55))) #(". To get\nrid of the locale warning see " 0 39 (:parent #51)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #57))) #(".\n" 0 2 (:parent #51))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #37]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #43))) (src-block (:standard-properties [3721 3721 nil nil 3826 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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #45))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("#+begin" 0 7 (:parent #46)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("src" 0 3 (:parent #50))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #46)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #46)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #46)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("src" 0 3 (:parent #56))) #("bash\n" 0 5 (:parent #46))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("To test whether this is working try:\n" 0 37 (:parent #47))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("#+begin" 0 7 (:parent #48)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("src" 0 3 (:parent #52))) #("bash\n#+end" 0 10 (:parent #48)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("src" 0 3 (:parent #54))) #("bash\n" 0 5 (:parent #48))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #38]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #44))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #41] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("by pasting it into the command\n" 0 31 (:parent #46))) (src-block (:standard-properties [4526 4526 nil nil 4579 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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("and hit Ctrl-D.\n" 0 16 (:parent #48))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #49))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #39]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #45))) (src-block (:standard-properties [4832 4832 nil nil 4951 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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #47))) (src-block (:standard-properties [5004 5004 nil nil 5194 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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #49)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #49]) #("root" 0 4 (:parent #53))) #(".config/guix/latest override).\n" 0 31 (:parent #49))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("And install with\n" 0 17 (:parent #50))) (src-block (:standard-properties [5321 5321 nil nil 5491 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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #52))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #53))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #54))) (src-block (:standard-properties [5961 5961 nil nil 6140 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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #56))) (src-block (:standard-properties [6209 6209 nil nil 6250 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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #58)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #58] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #58))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #59)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #33]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("GNU Guix allows for " 0 20 (:parent #39)) (link (:standard-properties [6584 nil 6653 6676 6679 1 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/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #43))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #39))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #36] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #41)) (link (:standard-properties [7007 nil 7112 7122 7124 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/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #45))) #(".\n" 0 2 (:parent #41))) (paragraph (:standard-properties [7127 7127 7127 7190 7191 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #42))) (fixed-width (:standard-properties [7191 7191 nil nil 7247 2 nil nil nil nil nil nil nil nil # nil nil #36] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [7247 7247 7247 7250 7251 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("So\n" 0 3 (:parent #44))) (paragraph (:standard-properties [7251 7251 7251 7637 7638 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("#+begin" 0 7 (:parent #45)) (subscript (:standard-properties [7258 nil 7259 7262 7263 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("src" 0 3 (:parent #49))) #("sh :lang bash\n#+begin" 0 23 (:parent #45)) (subscript (:standard-properties [7286 nil 7287 7290 7291 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("src" 0 3 (:parent #51))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #45)) (subscript (:standard-properties [7331 nil 7332 7339 7339 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #53))) (subscript (:standard-properties [7339 nil 7340 7344 7344 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("PATH" 0 4 (:parent #54))) #("=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork\ngenenetwork1 1.0-d622c803b out ../guix-bioinformatics/gn/packages/bioinformatics.scm:163:2\ngenenetwork2 2.0-9e9475053 out ../guix-bioinformatics/gn/packages/bioinformatics.scm:215:2\n#+end" 0 272 (:parent #45)) (subscript (:standard-properties [7616 nil 7617 7620 7621 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("src" 0 3 (:parent #56))) #("sh :lang bash\n" 0 16 (:parent #45))) (paragraph (:standard-properties [7638 7638 7638 7651 7652 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("Install with\n" 0 13 (:parent #46))) (paragraph (:standard-properties [7652 7652 7652 7811 7812 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("#+begin" 0 7 (:parent #47)) (subscript (:standard-properties [7659 nil 7660 7663 7664 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("src" 0 3 (:parent #51))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #47)) (subscript (:standard-properties [7704 nil 7705 7712 7712 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #53))) (subscript (:standard-properties [7712 nil 7713 7717 7717 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PATH" 0 4 (:parent #54))) #("=../guix-bioinformatics ./pre-inst-env guix package -i genenetwork2\n#+end" 0 73 (:parent #47)) (subscript (:standard-properties [7790 nil 7791 7794 7795 1 nil nil nil nil nil nil nil nil # 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Press Ctrl-C to interrupt.\n" 0 186 (:parent #39))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("If you need more help we have another writeup in " 0 49 (:parent #40)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #44))) #(". To get\nrid of the locale warning see " 0 39 (:parent #40)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #46))) #(".\n" 0 2 (:parent #40))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #26]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #29]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #32))) (src-block (:standard-properties [3721 3721 nil nil 3826 1 nil nil nil nil nil nil nil nil # nil nil #29] :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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #34))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("#+begin" 0 7 (:parent #35)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #35] :use-brackets-p nil) #("src" 0 3 (:parent #39))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #35)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #35] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #35)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #35] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #35)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #35] :use-brackets-p nil) #("src" 0 3 (:parent #45))) #("bash\n" 0 5 (:parent #35))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("To test whether this is working try:\n" 0 37 (:parent #36))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("#+begin" 0 7 (:parent #37)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("src" 0 3 (:parent #41))) #("bash\n#+end" 0 10 (:parent #37)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("src" 0 3 (:parent #43))) #("bash\n" 0 5 (:parent #37))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #27]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #30]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #33))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #30] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("by pasting it into the command\n" 0 31 (:parent #35))) (src-block (:standard-properties [4526 4526 nil nil 4579 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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("and hit Ctrl-D.\n" 0 16 (:parent #37))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #38))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 0 27 (: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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #28]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #31]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #34))) (src-block (:standard-properties [4832 4832 nil nil 4951 1 nil nil nil nil nil nil nil nil # nil nil #31] :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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #36))) (src-block (:standard-properties [5004 5004 nil nil 5194 1 nil nil nil nil nil nil nil nil # nil nil #31] :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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #38)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #38]) #("root" 0 4 (:parent #42))) #(".config/guix/latest override).\n" 0 31 (:parent #38))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("And install with\n" 0 17 (:parent #39))) (src-block (:standard-properties [5321 5321 nil nil 5491 1 nil nil nil nil nil nil nil nil # nil nil #31] :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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #41))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #42))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #43))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #31] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #45))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #31] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #47)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #47))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #48)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # 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A configuration file for\nGeneNetwork (reverse proxy) port forwarding can be found in the source\nrepository under ./etc/nginx-genenetwork.conf. 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For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #359))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. 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Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #360))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("Once you have succeeded, you have to " 0 37 (:parent #361)) (link (:standard-properties [2447 nil 2523 2534 2537 1 nil nil nil nil nil nil nil nil # nil nil #361] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #365))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #361))) (src-block (:standard-properties [2688 2688 nil nil 2796 1 nil nil nil nil nil nil nil nil # nil nil #357] :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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("Which should show something like\n" 0 33 (:parent #363))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #357] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) 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The actual installation command of 'hello' is\n" 0 70 (:parent #366))) (src-block (:standard-properties [3022 3022 nil nil 3094 1 nil nil nil nil nil nil nil nil # nil nil #357] :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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #368))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("If you need more help we have another writeup in " 0 49 (:parent #369)) (link (:standard-properties [3330 nil 3414 3424 3426 0 nil nil nil nil nil nil nil nil # nil nil #369] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #373))) #(". To get\nrid of the locale warning see " 0 39 (:parent #369)) (link (:standard-properties [3465 nil 3540 3550 3552 0 nil nil nil nil nil nil nil nil # nil nil #369] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #375))) #(".\n" 0 2 (:parent #369))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (:parent #355))) :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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #355]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #361))) (src-block (:standard-properties [3721 3721 nil nil 3826 1 nil nil nil nil nil nil nil nil # nil nil #358] :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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #363))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("#+begin" 0 7 (:parent #364)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #364] :use-brackets-p nil) #("src" 0 3 (:parent #368))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #364)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #364] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #364)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #364] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #364)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #364] :use-brackets-p nil) #("src" 0 3 (:parent #374))) #("bash\n" 0 5 (:parent #364))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("To test whether this is working try:\n" 0 37 (:parent #365))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("#+begin" 0 7 (:parent #366)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("src" 0 3 (:parent #370))) #("bash\n#+end" 0 10 (:parent #366)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("src" 0 3 (:parent #372))) #("bash\n" 0 5 (:parent #366))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #356]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #359]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #362))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #359] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("by pasting it into the command\n" 0 31 (:parent #364))) (src-block (:standard-properties [4526 4526 nil nil 4579 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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("and hit Ctrl-D.\n" 0 16 (:parent #366))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #367))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 0 27 (: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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #357]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #360]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #363))) (src-block (:standard-properties [4832 4832 nil nil 4951 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #365))) (src-block (:standard-properties [5004 5004 nil nil 5194 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #367)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #367]) #("root" 0 4 (:parent #371))) #(".config/guix/latest override).\n" 0 31 (:parent #367))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("And install with\n" 0 17 (:parent #368))) (src-block (:standard-properties [5321 5321 nil nil 5491 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #370))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #371))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #372))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #374))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #376)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #376] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #376))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #377)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #351]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #354]) #("GNU Guix allows for " 0 20 (:parent #357)) (link (:standard-properties [6584 nil 6653 6676 6679 1 nil nil nil nil nil nil nil nil # nil nil #357] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #361))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #357))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #354] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # 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A configuration file for\nGeneNetwork (reverse proxy) port forwarding can be found in the source\nrepository under ./etc/nginx-genenetwork.conf. 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nil nil #363]) #("#+begin" 0 7 (:parent #373)) (subscript (:standard-properties [13355 nil 13356 13359 13360 1 nil nil nil nil nil nil nil nil # nil nil #373] :use-brackets-p nil) #("src" 0 3 (:parent #377))) #("bash\ngenenetwork2\n#+end" 0 23 (:parent #373)) (subscript (:standard-properties [13383 nil 13384 13387 13388 1 nil nil nil nil nil nil nil nil # nil nil #373] :use-brackets-p nil) #("src" 0 3 (:parent #379))) #("bash\n" 0 5 (:parent #373))))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((plain-list (:standard-properties [135 135 135 1129 1130 1 nil planning nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 616) (249 3 "- " nil nil nil 312) (312 3 "- " nil nil nil 372) (372 3 "- " nil nil nil 466) (466 3 "- " nil nil nil 550) (550 3 "- " nil nil nil 616) (616 1 "- " nil nil nil 671) (671 1 "- " nil nil nil 710) (710 1 "- " nil nil nil 885) (755 3 "- " nil nil nil 816) (816 3 "- " nil nil nil 885) (885 1 "- " nil nil nil 1129) (1012 3 "- " nil nil nil 1067) (1067 3 "- " nil nil nil 1102) (1102 3 "- " nil nil nil 1129)) (section (:standard-properties [135 135 135 1130 1130 0 nil section nil nil nil 135 1130 nil # nil nil (headline (:standard-properties [57 57 135 1130 1130 0 (:title) nil nil nil nil 137 1128 1 # nil nil (org-data (:standard-properties [1 1 1 13393 13393 0 nil org-data nil nil nil 3 13393 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 57 57 0 nil first-section nil nil nil 1 57 nil # nil nil #15]) (keyword (:standard-properties [1 1 nil nil 57 1 nil top-comment nil nil nil nil nil nil # nil nil #18] :key "TITLE" :value "Installing GeneNetwork services with GNU Guix"))) #10 (headline (:standard-properties [1130 1130 1146 1409 1409 0 (:title) nil nil nil nil 1148 1407 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 [1146 1146 1146 1409 1409 0 nil section nil nil nil 1146 1409 nil # nil nil #20]) (paragraph (:standard-properties [1146 1146 1146 1408 1409 1 nil planning nil nil nil nil nil nil # nil nil #23]) #("Large system deployments tend to get very complex. In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #26)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #30))) #("and the main " 0 13 (:parent #26)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #26] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #26))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #15] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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) (headline (:standard-properties [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (: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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #24]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #27]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #30))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. If you use a virtual machine we recommend to use at least\ndouble.\n" 0 141 (:parent #31))))) (headline (:standard-properties [1928 1928 1957 3555 3555 0 (:title) nil nil nil nil 1959 3553 2 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 27) t] :title (#("Step 1: Install GNU Guix" 0 24 (: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 [1957 1957 1957 3555 3555 0 nil section nil nil nil 1957 3555 nil # nil nil #25]) (paragraph (:standard-properties [1957 1957 1957 2409 2410 1 nil planning nil nil nil nil nil nil # nil nil #28]) #("Fetch the GNU Guix binary from " 0 31 (:parent #31)) (link (:standard-properties [1988 nil 2035 2039 2042 1 nil nil nil nil nil nil nil nil # nil nil #31] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/download/" :format bracket :raw-link "https://www.gnu.org/software/guix/download/" :application nil :search-option nil) #("here" 0 4 (:parent #35))) #("(middle panel) and follow\n" 0 26 (:parent #31)) (link (:standard-properties [2068 nil 2147 2159 2161 0 nil nil nil nil nil nil nil nil # nil nil #31] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :format bracket :raw-link "https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :application nil :search-option nil) #("instructions" 0 12 (:parent #37))) #(". Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #31))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("Once you have succeeded, you have to " 0 37 (:parent #32)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #36))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #32))) (src-block (:standard-properties [2688 2688 nil nil 2796 1 nil nil nil nil nil nil nil nil # nil nil #28] :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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("Which should show something like\n" 0 33 (:parent #34))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #28] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) (paragraph (:standard-properties [2940 2940 2940 2950 2951 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("#+end" 0 5 (:parent #36)) (subscript (:standard-properties [2945 nil 2946 2949 2949 0 nil nil nil nil nil nil nil nil # nil nil #36] :use-brackets-p nil) #("src" 0 3 (:parent #40))) #("\n" 0 1 (:parent #36))) (paragraph (:standard-properties [2951 2951 2951 3021 3022 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("means binary installs. The actual installation command of 'hello' is\n" 0 70 (:parent #37))) (src-block (:standard-properties [3022 3022 nil nil 3094 1 nil nil nil nil nil nil nil nil # nil nil #28] :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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #39))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("If you need more help we have another writeup in " 0 49 (:parent #40)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #44))) #(". To get\nrid of the locale warning see " 0 39 (:parent #40)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #46))) #(".\n" 0 2 (:parent #40))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #26]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #29]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #32))) (src-block (:standard-properties [3721 3721 nil nil 3826 1 nil nil nil nil nil nil nil nil # nil nil #29] :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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #34))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("#+begin" 0 7 (:parent #35)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #35] :use-brackets-p nil) #("src" 0 3 (:parent #39))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #35)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #35] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #35)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #35] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #35)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #35] :use-brackets-p nil) #("src" 0 3 (:parent #45))) #("bash\n" 0 5 (:parent #35))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("To test whether this is working try:\n" 0 37 (:parent #36))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("#+begin" 0 7 (:parent #37)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("src" 0 3 (:parent #41))) #("bash\n#+end" 0 10 (:parent #37)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("src" 0 3 (:parent #43))) #("bash\n" 0 5 (:parent #37))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #27]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #30]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #33))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #30] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("by pasting it into the command\n" 0 31 (:parent #35))) (src-block (:standard-properties [4526 4526 nil nil 4579 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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("and hit Ctrl-D.\n" 0 16 (:parent #37))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #38))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 0 27 (: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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #28]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #31]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #34))) (src-block (:standard-properties [4832 4832 nil nil 4951 1 nil nil nil nil nil nil nil nil # nil nil #31] :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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #36))) (src-block (:standard-properties [5004 5004 nil nil 5194 1 nil nil nil nil nil nil nil nil # nil nil #31] :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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #38)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #38]) #("root" 0 4 (:parent #42))) #(".config/guix/latest override).\n" 0 31 (:parent #38))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("And install with\n" 0 17 (:parent #39))) (src-block (:standard-properties [5321 5321 nil nil 5491 1 nil nil nil nil nil nil nil nil # nil nil #31] :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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #41))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #42))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #43))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #31] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #45))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #31] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #47)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #47))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #48)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #22]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #25]) #("GNU Guix allows for " 0 20 (:parent #28)) (link (:standard-properties [6584 nil 6653 6676 6679 1 nil nil nil nil nil nil nil nil # nil nil #28] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #32))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #28))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #25] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # 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Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #32))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("Once you have succeeded, you have to " 0 37 (:parent #33)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #37))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #33))) (src-block (:standard-properties [2688 2688 nil nil 2796 1 nil nil nil nil nil nil nil nil # nil nil #29] :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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("Which should show something like\n" 0 33 (:parent #35))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #29] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) 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Press Ctrl-C to interrupt.\n" 0 186 (:parent #40))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("If you need more help we have another writeup in " 0 49 (:parent #41)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #45))) #(". To get\nrid of the locale warning see " 0 39 (:parent #41)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #47))) #(".\n" 0 2 (:parent #41))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #27]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #30]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. 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The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #43))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #44))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #32] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #46))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #32] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. 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These settings may\nnot reflect your system. To override settings create your own from a copy of\ndefault" 0 105 (:parent #40)) (subscript (:standard-properties [9068 nil 9069 9080 9081 1 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("settings.py" 0 11 (:parent #48))) #("and pass it into GN2 with\n" 0 26 (:parent #40))) (fixed-width (:standard-properties [9108 9108 nil nil 9151 2 nil nil nil nil nil nil nil nil # nil nil #32] :value "./bin/genenetwork2 $HOME/my_settings.py")) (paragraph (:standard-properties [9151 9151 9151 9296 9297 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("and everything " 0 15 (:parent #42)) (bold (:standard-properties [9166 nil 9167 9173 9175 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("should" 0 6 (:parent #46))) #("work (note the full path to the settings\nfile). 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In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #21)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #25))) #("and the main " 0 13 (:parent #21)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #21] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #21))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #10] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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) (headline (:standard-properties [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (: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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #19]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #22]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #25))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. If you use a virtual machine we recommend to use at least\ndouble.\n" 0 141 (:parent #26))))) (headline (:standard-properties [1928 1928 1957 3555 3555 0 (:title) nil nil nil nil 1959 3553 2 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 27) t] :title (#("Step 1: Install GNU Guix" 0 24 (: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 [1957 1957 1957 3555 3555 0 nil section nil nil nil 1957 3555 nil # nil nil #20]) (paragraph (:standard-properties [1957 1957 1957 2409 2410 1 nil planning nil nil nil nil nil nil # nil nil #23]) #("Fetch the GNU Guix binary from " 0 31 (:parent #26)) (link (:standard-properties [1988 nil 2035 2039 2042 1 nil nil nil nil nil nil nil nil # nil nil #26] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/download/" :format bracket :raw-link "https://www.gnu.org/software/guix/download/" :application nil :search-option nil) #("here" 0 4 (:parent #30))) #("(middle panel) and follow\n" 0 26 (:parent #26)) (link (:standard-properties [2068 nil 2147 2159 2161 0 nil nil nil nil nil nil nil nil # nil nil #26] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :format bracket :raw-link "https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :application nil :search-option nil) #("instructions" 0 12 (:parent #32))) #(". Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #26))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("Once you have succeeded, you have to " 0 37 (:parent #27)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #31))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #27))) (src-block (:standard-properties [2688 2688 nil nil 2796 1 nil nil nil nil nil nil nil nil # nil nil #23] :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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("Which should show something like\n" 0 33 (:parent #29))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #23] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) (paragraph (:standard-properties [2940 2940 2940 2950 2951 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("#+end" 0 5 (:parent #31)) (subscript (:standard-properties [2945 nil 2946 2949 2949 0 nil nil nil nil nil nil nil nil # nil nil #31] :use-brackets-p nil) #("src" 0 3 (:parent #35))) #("\n" 0 1 (:parent #31))) (paragraph (:standard-properties [2951 2951 2951 3021 3022 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("means binary installs. The actual installation command of 'hello' is\n" 0 70 (:parent #32))) (src-block (:standard-properties [3022 3022 nil nil 3094 1 nil nil nil nil nil nil nil nil # nil nil #23] :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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #34))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("If you need more help we have another writeup in " 0 49 (:parent #35)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #39))) #(". To get\nrid of the locale warning see " 0 39 (:parent #35)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #41))) #(".\n" 0 2 (:parent #35))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #21]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #27))) (src-block (:standard-properties [3721 3721 nil nil 3826 1 nil nil nil nil nil nil nil nil # nil nil #24] :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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #29))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("#+begin" 0 7 (:parent #30)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #30] :use-brackets-p nil) #("src" 0 3 (:parent #34))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #30)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #30] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #30)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #30] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #30)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #30] :use-brackets-p nil) #("src" 0 3 (:parent #40))) #("bash\n" 0 5 (:parent #30))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("To test whether this is working try:\n" 0 37 (:parent #31))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("#+begin" 0 7 (:parent #32)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("src" 0 3 (:parent #36))) #("bash\n#+end" 0 10 (:parent #32)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("src" 0 3 (:parent #38))) #("bash\n" 0 5 (:parent #32))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #22]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #25]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #28))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #25] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("by pasting it into the command\n" 0 31 (:parent #30))) (src-block (:standard-properties [4526 4526 nil nil 4579 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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("and hit Ctrl-D.\n" 0 16 (:parent #32))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #33))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 0 27 (: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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #23]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #26]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #29))) (src-block (:standard-properties [4832 4832 nil nil 4951 1 nil nil nil nil nil nil nil nil # nil nil #26] :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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #31))) (src-block (:standard-properties [5004 5004 nil nil 5194 1 nil nil nil nil nil nil nil nil # nil nil #26] :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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #33)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #33]) #("root" 0 4 (:parent #37))) #(".config/guix/latest override).\n" 0 31 (:parent #33))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("And install with\n" 0 17 (:parent #34))) (src-block (:standard-properties [5321 5321 nil nil 5491 1 nil nil nil nil nil nil nil nil # nil nil #26] :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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #36))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #37))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #38))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #26] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #40))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #26] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #42)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #42))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #43)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #17]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #20]) #("GNU Guix allows for " 0 20 (:parent #23)) (link (:standard-properties [6584 nil 6653 6676 6679 1 nil nil nil nil nil nil nil nil # nil nil #23] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #27))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #23))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #20] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #25)) (link (:standard-properties [7007 nil 7112 7122 7124 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/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #29))) #(".\n" 0 2 (:parent #25))) (paragraph (:standard-properties [7127 7127 7127 7190 7191 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #26))) (fixed-width (:standard-properties [7191 7191 nil nil 7247 2 nil nil nil nil nil nil nil nil # nil nil #20] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [7247 7247 7247 7250 7251 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("So\n" 0 3 (:parent #28))) (paragraph (:standard-properties [7251 7251 7251 7637 7638 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("#+begin" 0 7 (:parent #29)) (subscript (:standard-properties [7258 nil 7259 7262 7263 1 nil nil nil nil nil nil nil nil # nil nil #29] :use-brackets-p nil) #("src" 0 3 (:parent #33))) #("sh :lang bash\n#+begin" 0 23 (:parent #29)) (subscript (:standard-properties [7286 nil 7287 7290 7291 1 nil nil nil nil nil nil nil nil # nil nil #29] :use-brackets-p nil) #("src" 0 3 (:parent #35))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #29)) (subscript (:standard-properties [7331 nil 7332 7339 7339 0 nil nil nil nil nil nil nil nil # nil nil #29] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #37))) (subscript (:standard-properties [7339 nil 7340 7344 7344 0 nil nil nil nil nil nil nil nil # nil nil #29] :use-brackets-p nil) #("PATH" 0 4 (:parent #38))) #("=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork\ngenenetwork1 1.0-d622c803b out ../guix-bioinformatics/gn/packages/bioinformatics.scm:163:2\ngenenetwork2 2.0-9e9475053 out ../guix-bioinformatics/gn/packages/bioinformatics.scm:215:2\n#+end" 0 272 (:parent #29)) (subscript (:standard-properties [7616 nil 7617 7620 7621 1 nil nil nil nil nil nil nil nil # 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In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #355)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #359))) #("and the main " 0 13 (:parent #355)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #355] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #355))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #344] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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) (headline (:standard-properties [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (:parent #353))) :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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #353]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #356]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #359))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. If you use a virtual machine we recommend to use at least\ndouble.\n" 0 141 (:parent #360))))) (headline (:standard-properties [1928 1928 1957 3555 3555 0 (:title) nil nil nil nil 1959 3553 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 27) t] :title (#("Step 1: Install GNU Guix" 0 24 (:parent #354))) :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 [1957 1957 1957 3555 3555 0 nil section nil nil nil 1957 3555 nil # nil nil #354]) (paragraph (:standard-properties [1957 1957 1957 2409 2410 1 nil planning nil nil nil nil nil nil # nil nil #357]) #("Fetch the GNU Guix binary from " 0 31 (:parent #360)) (link (:standard-properties [1988 nil 2035 2039 2042 1 nil nil nil nil nil nil nil nil # nil nil #360] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/download/" :format bracket :raw-link "https://www.gnu.org/software/guix/download/" :application nil :search-option nil) #("here" 0 4 (:parent #364))) #("(middle panel) and follow\n" 0 26 (:parent #360)) (link (:standard-properties [2068 nil 2147 2159 2161 0 nil nil nil nil nil nil nil nil # nil nil #360] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :format bracket :raw-link "https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :application nil :search-option nil) #("instructions" 0 12 (:parent #366))) #(". Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #360))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("Once you have succeeded, you have to " 0 37 (:parent #361)) (link (:standard-properties [2447 nil 2523 2534 2537 1 nil nil nil nil nil nil nil nil # nil nil #361] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #365))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #361))) (src-block (:standard-properties [2688 2688 nil nil 2796 1 nil nil nil nil nil nil nil nil # nil nil #357] :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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("Which should show something like\n" 0 33 (:parent #363))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #357] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) (paragraph (:standard-properties [2940 2940 2940 2950 2951 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("#+end" 0 5 (:parent #365)) (subscript (:standard-properties [2945 nil 2946 2949 2949 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("src" 0 3 (:parent #369))) #("\n" 0 1 (:parent #365))) (paragraph (:standard-properties [2951 2951 2951 3021 3022 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("means binary installs. The actual installation command of 'hello' is\n" 0 70 (:parent #366))) (src-block (:standard-properties [3022 3022 nil nil 3094 1 nil nil nil nil nil nil nil nil # nil nil #357] :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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #368))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("If you need more help we have another writeup in " 0 49 (:parent #369)) (link (:standard-properties [3330 nil 3414 3424 3426 0 nil nil nil nil nil nil nil nil # nil nil #369] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #373))) #(". To get\nrid of the locale warning see " 0 39 (:parent #369)) (link (:standard-properties [3465 nil 3540 3550 3552 0 nil nil nil nil nil nil nil nil # nil nil #369] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #375))) #(".\n" 0 2 (:parent #369))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (:parent #355))) :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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #355]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #361))) (src-block (:standard-properties [3721 3721 nil nil 3826 1 nil nil nil nil nil nil nil nil # nil nil #358] :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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #363))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("#+begin" 0 7 (:parent #364)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #364] :use-brackets-p nil) #("src" 0 3 (:parent #368))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #364)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #364] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #364)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #364] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #364)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #364] :use-brackets-p nil) #("src" 0 3 (:parent #374))) #("bash\n" 0 5 (:parent #364))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("To test whether this is working try:\n" 0 37 (:parent #365))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("#+begin" 0 7 (:parent #366)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("src" 0 3 (:parent #370))) #("bash\n#+end" 0 10 (:parent #366)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("src" 0 3 (:parent #372))) #("bash\n" 0 5 (:parent #366))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #356]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #359]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #362))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #359] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("by pasting it into the command\n" 0 31 (:parent #364))) (src-block (:standard-properties [4526 4526 nil nil 4579 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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("and hit Ctrl-D.\n" 0 16 (:parent #366))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #367))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 0 27 (: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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #357]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #360]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #363))) (src-block (:standard-properties [4832 4832 nil nil 4951 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #365))) (src-block (:standard-properties [5004 5004 nil nil 5194 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #367)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #367]) #("root" 0 4 (:parent #371))) #(".config/guix/latest override).\n" 0 31 (:parent #367))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("And install with\n" 0 17 (:parent #368))) (src-block (:standard-properties [5321 5321 nil nil 5491 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #370))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #371))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #372))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #374))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #376)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #376] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #376))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #377)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #351]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #354]) #("GNU Guix allows for " 0 20 (:parent #357)) (link (:standard-properties [6584 nil 6653 6676 6679 1 nil nil nil nil nil nil nil nil # nil nil #357] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #361))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #357))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #354] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #359)) (link (:standard-properties [7007 nil 7112 7122 7124 0 nil nil nil nil nil nil nil nil # nil nil #359] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #363))) #(".\n" 0 2 (:parent #359))) (paragraph (:standard-properties [7127 7127 7127 7190 7191 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #360))) (fixed-width (:standard-properties [7191 7191 nil nil 7247 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [7247 7247 7247 7250 7251 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("So\n" 0 3 (:parent #362))) (paragraph (:standard-properties [7251 7251 7251 7637 7638 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("#+begin" 0 7 (:parent #363)) (subscript (:standard-properties [7258 nil 7259 7262 7263 1 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("src" 0 3 (:parent #367))) #("sh :lang bash\n#+begin" 0 23 (:parent #363)) (subscript (:standard-properties [7286 nil 7287 7290 7291 1 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("src" 0 3 (:parent #369))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #363)) (subscript (:standard-properties [7331 nil 7332 7339 7339 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #371))) (subscript (:standard-properties [7339 nil 7340 7344 7344 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("PATH" 0 4 (:parent #372))) #("=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork\ngenenetwork1 1.0-d622c803b out ../guix-bioinformatics/gn/packages/bioinformatics.scm:163:2\ngenenetwork2 2.0-9e9475053 out ../guix-bioinformatics/gn/packages/bioinformatics.scm:215:2\n#+end" 0 272 (:parent #363)) (subscript (:standard-properties [7616 nil 7617 7620 7621 1 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("src" 0 3 (:parent #374))) #("sh :lang bash\n" 0 16 (:parent #363))) (paragraph (:standard-properties [7638 7638 7638 7651 7652 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("Install with\n" 0 13 (:parent #364))) (paragraph (:standard-properties [7652 7652 7652 7811 7812 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("#+begin" 0 7 (:parent #365)) (subscript (:standard-properties [7659 nil 7660 7663 7664 1 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("src" 0 3 (:parent #369))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #365)) (subscript (:standard-properties [7704 nil 7705 7712 7712 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #371))) (subscript (:standard-properties [7712 nil 7713 7717 7717 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("PATH" 0 4 (:parent #372))) #("=../guix-bioinformatics ./pre-inst-env guix package -i genenetwork2\n#+end" 0 73 (:parent #365)) (subscript (:standard-properties [7790 nil 7791 7794 7795 1 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("src" 0 3 (:parent #374))) #("sh :lang bash\n" 0 16 (:parent #365))))) (headline (:standard-properties [7812 7812 7830 7977 7977 0 (:title) nil nil nil nil 7832 7975 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 16) t] :title (#("Create archive" 0 14 (: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 [7830 7830 7830 7977 7977 0 nil section nil nil nil 7830 7977 nil # nil nil #352]) (fixed-width (:standard-properties [7830 7830 nil nil 7977 3 nil planning nil nil nil nil nil nil # nil nil #355] :value "env GUIX_PACKAGE_PATH=../../genenetwork/guix-bioinformatics/ ./pre-inst-env guix archive --export -r genenetwork2 > guix_gn2-2.0-9e9475053.nar")))) (headline (:standard-properties [7977 7977 7998 11645 11645 0 (:title) nil nil nil nil 8000 11643 1 # 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nil nil #366] :use-brackets-p nil) #("src" 0 3 (:parent #378))) #("bash\n" 0 5 (:parent #366))) (paragraph (:standard-properties [12481 12481 12481 12518 12519 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("Note the use of ./pre-inst-env here!\n" 0 37 (:parent #367))) (paragraph (:standard-properties [12519 12519 12519 12606 12607 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("Actually, it should be the same installation as in step 4, so nothing\ngets downloaded.\n" 0 87 (:parent #368))))) (headline (:standard-properties [12607 12607 12619 13393 13393 0 (:title) nil nil nil nil 12621 13391 2 # nil nil #354] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 10) t] :title (#("Run GN2" 0 7 (: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 [12619 12619 12619 13393 13393 0 nil section nil nil nil 12619 13393 nil # 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nil nil #363]) #("#+begin" 0 7 (:parent #373)) (subscript (:standard-properties [13355 nil 13356 13359 13360 1 nil nil nil nil nil nil nil nil # nil nil #373] :use-brackets-p nil) #("src" 0 3 (:parent #377))) #("bash\ngenenetwork2\n#+end" 0 23 (:parent #373)) (subscript (:standard-properties [13383 nil 13384 13387 13388 1 nil nil nil nil nil nil nil nil # nil nil #373] :use-brackets-p nil) #("src" 0 3 (:parent #379))) #("bash\n" 0 5 (:parent #373))))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((section (:standard-properties [135 135 135 1130 1130 0 nil section nil nil nil 135 1130 nil # nil nil (headline (:standard-properties [57 57 135 1130 1130 0 (:title) nil nil nil nil 137 1128 1 # nil nil (org-data (:standard-properties [1 1 1 13393 13393 0 nil org-data nil nil nil 3 13393 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 57 57 0 nil first-section nil nil nil 1 57 nil # nil nil #10]) (keyword (:standard-properties [1 1 nil nil 57 1 nil top-comment nil nil nil nil nil nil # nil nil #13] :key "TITLE" :value "Installing GeneNetwork services with GNU Guix"))) #5 (headline (:standard-properties [1130 1130 1146 1409 1409 0 (:title) nil nil nil nil 1148 1407 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 [1146 1146 1146 1409 1409 0 nil section nil nil nil 1146 1409 nil # nil nil #15]) (paragraph (:standard-properties [1146 1146 1146 1408 1409 1 nil planning nil nil nil nil nil nil # nil nil #18]) #("Large system deployments tend to get very complex. In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #21)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #25))) #("and the main " 0 13 (:parent #21)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #21] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #21))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #10] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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) (headline (:standard-properties [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (: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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #19]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #22]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #25))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. If you use a virtual machine we recommend to use at least\ndouble.\n" 0 141 (:parent #26))))) (headline (:standard-properties [1928 1928 1957 3555 3555 0 (:title) nil nil nil nil 1959 3553 2 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 27) t] :title (#("Step 1: Install GNU Guix" 0 24 (: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 [1957 1957 1957 3555 3555 0 nil section nil nil nil 1957 3555 nil # nil nil #20]) (paragraph (:standard-properties [1957 1957 1957 2409 2410 1 nil planning nil nil nil nil nil nil # nil nil #23]) #("Fetch the GNU Guix binary from " 0 31 (:parent #26)) (link (:standard-properties [1988 nil 2035 2039 2042 1 nil nil nil nil nil nil nil nil # nil nil #26] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/download/" :format bracket :raw-link "https://www.gnu.org/software/guix/download/" :application nil :search-option nil) #("here" 0 4 (:parent #30))) #("(middle panel) and follow\n" 0 26 (:parent #26)) (link (:standard-properties [2068 nil 2147 2159 2161 0 nil nil nil nil nil nil nil nil # nil nil #26] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :format bracket :raw-link "https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :application nil :search-option nil) #("instructions" 0 12 (:parent #32))) #(". Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #26))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("Once you have succeeded, you have to " 0 37 (:parent #27)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #31))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #27))) (src-block (:standard-properties [2688 2688 nil nil 2796 1 nil nil nil nil nil nil nil nil # nil nil #23] :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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("Which should show something like\n" 0 33 (:parent #29))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #23] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) 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The actual installation command of 'hello' is\n" 0 70 (:parent #32))) (src-block (:standard-properties [3022 3022 nil nil 3094 1 nil nil nil nil nil nil nil nil # nil nil #23] :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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #34))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("If you need more help we have another writeup in " 0 49 (:parent #35)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #39))) #(". To get\nrid of the locale warning see " 0 39 (:parent #35)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #41))) #(".\n" 0 2 (:parent #35))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #21]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #27))) (src-block (:standard-properties [3721 3721 nil nil 3826 1 nil nil nil nil nil nil nil nil # nil nil #24] :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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #29))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("#+begin" 0 7 (:parent #30)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #30] :use-brackets-p nil) #("src" 0 3 (:parent #34))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #30)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #30] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #30)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #30] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #30)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #30] :use-brackets-p nil) #("src" 0 3 (:parent #40))) #("bash\n" 0 5 (:parent #30))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("To test whether this is working try:\n" 0 37 (:parent #31))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("#+begin" 0 7 (:parent #32)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("src" 0 3 (:parent #36))) #("bash\n#+end" 0 10 (:parent #32)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("src" 0 3 (:parent #38))) #("bash\n" 0 5 (:parent #32))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #22]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #25]) #("GN2 has its own GNU Guix binary distribution server. 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The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #37))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #38))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #26] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #40))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #26] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. 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These settings may\nnot reflect your system. To override settings create your own from a copy of\ndefault" 0 105 (:parent #34)) (subscript (:standard-properties [9068 nil 9069 9080 9081 1 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("settings.py" 0 11 (:parent #42))) #("and pass it into GN2 with\n" 0 26 (:parent #34))) (fixed-width (:standard-properties [9108 9108 nil nil 9151 2 nil nil nil nil nil nil nil nil # nil nil #26] :value "./bin/genenetwork2 $HOME/my_settings.py")) (paragraph (:standard-properties [9151 9151 9151 9296 9297 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("and everything " 0 15 (:parent #36)) (bold (:standard-properties [9166 nil 9167 9173 9175 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("should" 0 6 (:parent #40))) #("work (note the full path to the settings\nfile). 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In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #22)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #26))) #("and the main " 0 13 (:parent #22)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #22] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #22))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #11] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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) (headline (:standard-properties [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #17] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (: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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #20]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #23]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #26))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. If you use a virtual machine we recommend to use at least\ndouble.\n" 0 141 (:parent #27))))) (headline (:standard-properties [1928 1928 1957 3555 3555 0 (:title) nil nil nil nil 1959 3553 2 # nil nil #17] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 27) t] :title (#("Step 1: Install GNU Guix" 0 24 (: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 [1957 1957 1957 3555 3555 0 nil section nil nil nil 1957 3555 nil # nil nil #21]) (paragraph (:standard-properties [1957 1957 1957 2409 2410 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("Fetch the GNU Guix binary from " 0 31 (:parent #27)) (link (:standard-properties [1988 nil 2035 2039 2042 1 nil nil nil nil nil nil nil nil # nil nil #27] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/download/" :format bracket :raw-link "https://www.gnu.org/software/guix/download/" :application nil :search-option nil) #("here" 0 4 (:parent #31))) #("(middle panel) and follow\n" 0 26 (:parent #27)) (link (:standard-properties [2068 nil 2147 2159 2161 0 nil nil nil nil nil nil nil nil # nil nil #27] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :format bracket :raw-link "https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :application nil :search-option nil) #("instructions" 0 12 (:parent #33))) #(". Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #27))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("Once you have succeeded, you have to " 0 37 (:parent #28)) (link (:standard-properties [2447 nil 2523 2534 2537 1 nil nil nil nil nil nil nil nil # nil nil #28] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #32))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #28))) (src-block (:standard-properties [2688 2688 nil nil 2796 1 nil nil nil nil nil nil nil nil # nil nil #24] :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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("Which should show something like\n" 0 33 (:parent #30))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #24] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) (paragraph (:standard-properties [2940 2940 2940 2950 2951 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("#+end" 0 5 (:parent #32)) (subscript (:standard-properties [2945 nil 2946 2949 2949 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("src" 0 3 (:parent #36))) #("\n" 0 1 (:parent #32))) (paragraph (:standard-properties [2951 2951 2951 3021 3022 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("means binary installs. The actual installation command of 'hello' is\n" 0 70 (:parent #33))) (src-block (:standard-properties [3022 3022 nil nil 3094 1 nil nil nil nil nil nil nil nil # nil nil #24] :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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #35))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("If you need more help we have another writeup in " 0 49 (:parent #36)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #40))) #(". To get\nrid of the locale warning see " 0 39 (:parent #36)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #42))) #(".\n" 0 2 (:parent #36))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #17] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #22]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #25]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #28))) (src-block (:standard-properties [3721 3721 nil nil 3826 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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #30))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("#+begin" 0 7 (:parent #31)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #31] :use-brackets-p nil) #("src" 0 3 (:parent #35))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #31)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #31] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #31)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #31] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #31)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #31] :use-brackets-p nil) #("src" 0 3 (:parent #41))) #("bash\n" 0 5 (:parent #31))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("To test whether this is working try:\n" 0 37 (:parent #32))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("#+begin" 0 7 (:parent #33)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("src" 0 3 (:parent #37))) #("bash\n#+end" 0 10 (:parent #33)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("src" 0 3 (:parent #39))) #("bash\n" 0 5 (:parent #33))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #17] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #23]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #26]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #29))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #26] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("by pasting it into the command\n" 0 31 (:parent #31))) (src-block (:standard-properties [4526 4526 nil nil 4579 1 nil nil nil nil nil nil nil nil # nil nil #26] :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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("and hit Ctrl-D.\n" 0 16 (:parent #33))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #34))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #17] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #24]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #27]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #30))) (src-block (:standard-properties [4832 4832 nil nil 4951 1 nil nil nil nil nil nil nil nil # nil nil #27] :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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #32))) (src-block (:standard-properties [5004 5004 nil nil 5194 1 nil nil nil nil nil nil nil nil # nil nil #27] :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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #34)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #34]) #("root" 0 4 (:parent #38))) #(".config/guix/latest override).\n" 0 31 (:parent #34))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("And install with\n" 0 17 (:parent #35))) (src-block (:standard-properties [5321 5321 nil nil 5491 1 nil nil nil nil nil nil nil nil # nil nil #27] :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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #37))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #38))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #39))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #27] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #41))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #27] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #43)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #43))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #44)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #18]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #21]) #("GNU Guix allows for " 0 20 (:parent #24)) (link (:standard-properties [6584 nil 6653 6676 6679 1 nil nil nil nil nil nil nil nil # nil nil #24] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #28))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #24))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #21] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #26)) (link (:standard-properties [7007 nil 7112 7122 7124 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/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #30))) #(".\n" 0 2 (:parent #26))) (paragraph (:standard-properties [7127 7127 7127 7190 7191 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #27))) (fixed-width (:standard-properties [7191 7191 nil nil 7247 2 nil nil nil nil nil nil nil nil # nil nil #21] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [7247 7247 7247 7250 7251 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("So\n" 0 3 (:parent #29))) (paragraph (:standard-properties [7251 7251 7251 7637 7638 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("#+begin" 0 7 (:parent #30)) (subscript (:standard-properties [7258 nil 7259 7262 7263 1 nil nil nil nil nil nil nil nil # nil nil #30] :use-brackets-p nil) #("src" 0 3 (:parent #34))) #("sh :lang bash\n#+begin" 0 23 (:parent #30)) (subscript (:standard-properties [7286 nil 7287 7290 7291 1 nil nil nil nil nil nil nil nil # nil nil #30] :use-brackets-p nil) #("src" 0 3 (:parent #36))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #30)) (subscript (:standard-properties [7331 nil 7332 7339 7339 0 nil nil nil nil nil nil nil nil # nil nil #30] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #38))) (subscript (:standard-properties [7339 nil 7340 7344 7344 0 nil nil nil nil nil nil nil nil # nil nil #30] :use-brackets-p nil) #("PATH" 0 4 (:parent #39))) #("=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork\ngenenetwork1 1.0-d622c803b out ../guix-bioinformatics/gn/packages/bioinformatics.scm:163:2\ngenenetwork2 2.0-9e9475053 out ../guix-bioinformatics/gn/packages/bioinformatics.scm:215:2\n#+end" 0 272 (:parent #30)) (subscript (:standard-properties [7616 nil 7617 7620 7621 1 nil nil nil nil nil nil nil nil # 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Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #21))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("Once you have succeeded, you have to " 0 37 (:parent #22)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #26))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #22))) (src-block (:standard-properties [2688 2688 nil nil 2796 1 nil nil nil nil nil nil nil nil # nil nil #18] :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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("Which should show something like\n" 0 33 (:parent #24))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #18] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) 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Press Ctrl-C to interrupt.\n" 0 186 (:parent #29))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("If you need more help we have another writeup in " 0 49 (:parent #30)) (link (:standard-properties [3330 nil 3414 3424 3426 0 nil nil nil nil nil nil nil nil # nil nil #30] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #34))) #(". To get\nrid of the locale warning see " 0 39 (:parent #30)) (link (:standard-properties [3465 nil 3540 3550 3552 0 nil nil nil nil nil nil nil nil # nil nil #30] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #36))) #(".\n" 0 2 (:parent #30))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #16]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #19]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. 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The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #32))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #33))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #21] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #35))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #21] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #37)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #37))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #38)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # 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These settings may\nnot reflect your system. To override settings create your own from a copy of\ndefault" 0 105 (:parent #29)) (subscript (:standard-properties [9068 nil 9069 9080 9081 1 nil nil nil nil nil nil nil nil # nil nil #29] :use-brackets-p nil) #("settings.py" 0 11 (:parent #37))) #("and pass it into GN2 with\n" 0 26 (:parent #29))) (fixed-width (:standard-properties [9108 9108 nil nil 9151 2 nil nil nil nil nil nil nil nil # nil nil #21] :value "./bin/genenetwork2 $HOME/my_settings.py")) (paragraph (:standard-properties [9151 9151 9151 9296 9297 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("and everything " 0 15 (:parent #31)) (bold (:standard-properties [9166 nil 9167 9173 9175 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("should" 0 6 (:parent #35))) #("work (note the full path to the settings\nfile). 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Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #360))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("Once you have succeeded, you have to " 0 37 (:parent #361)) (link (:standard-properties [2447 nil 2523 2534 2537 1 nil nil nil nil nil nil nil nil # nil nil #361] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #365))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #361))) (src-block (:standard-properties [2688 2688 nil nil 2796 1 nil nil nil nil nil nil nil nil # nil nil #357] :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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("Which should show something like\n" 0 33 (:parent #363))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #357] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) 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The actual installation command of 'hello' is\n" 0 70 (:parent #366))) (src-block (:standard-properties [3022 3022 nil nil 3094 1 nil nil nil nil nil nil nil nil # nil nil #357] :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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #368))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("If you need more help we have another writeup in " 0 49 (:parent #369)) (link (:standard-properties [3330 nil 3414 3424 3426 0 nil nil nil nil nil nil nil nil # nil nil #369] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #373))) #(". To get\nrid of the locale warning see " 0 39 (:parent #369)) (link (:standard-properties [3465 nil 3540 3550 3552 0 nil nil nil nil nil nil nil nil # nil nil #369] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #375))) #(".\n" 0 2 (:parent #369))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (:parent #355))) :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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #355]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #361))) (src-block (:standard-properties [3721 3721 nil nil 3826 1 nil nil nil nil nil nil nil nil # nil nil #358] :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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #363))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("#+begin" 0 7 (:parent #364)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #364] :use-brackets-p nil) #("src" 0 3 (:parent #368))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #364)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #364] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #364)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #364] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #364)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #364] :use-brackets-p nil) #("src" 0 3 (:parent #374))) #("bash\n" 0 5 (:parent #364))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("To test whether this is working try:\n" 0 37 (:parent #365))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("#+begin" 0 7 (:parent #366)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("src" 0 3 (:parent #370))) #("bash\n#+end" 0 10 (:parent #366)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("src" 0 3 (:parent #372))) #("bash\n" 0 5 (:parent #366))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #356]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #359]) #("GN2 has its own GNU Guix binary distribution server. 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The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #371))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #372))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #374))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #376)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #376] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #376))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #377)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #351]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #354]) #("GNU Guix allows for " 0 20 (:parent #357)) (link (:standard-properties [6584 nil 6653 6676 6679 1 nil nil nil nil nil nil nil nil # nil nil #357] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #361))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #357))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #354] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # 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These settings may\nnot reflect your system. To override settings create your own from a copy of\ndefault" 0 105 (:parent #368)) (subscript (:standard-properties [9068 nil 9069 9080 9081 1 nil nil nil nil nil nil nil nil # nil nil #368] :use-brackets-p nil) #("settings.py" 0 11 (:parent #376))) #("and pass it into GN2 with\n" 0 26 (:parent #368))) (fixed-width (:standard-properties [9108 9108 nil nil 9151 2 nil nil nil nil nil nil nil nil # nil nil #360] :value "./bin/genenetwork2 $HOME/my_settings.py")) (paragraph (:standard-properties [9151 9151 9151 9296 9297 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("and everything " 0 15 (:parent #370)) (bold (:standard-properties [9166 nil 9167 9173 9175 1 nil nil nil nil nil nil nil nil # nil nil #370]) #("should" 0 6 (:parent #374))) #("work (note the full path to the settings\nfile). 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In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #16)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #20))) #("and the main " 0 13 (:parent #16)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #16] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #16))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #5] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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 [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (: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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #14]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #17]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #20))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. If you use a virtual machine we recommend to use at least\ndouble.\n" 0 141 (:parent #21))))) (headline (:standard-properties [1928 1928 1957 3555 3555 0 (:title) nil nil nil nil 1959 3553 2 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 27) t] :title (#("Step 1: Install GNU Guix" 0 24 (: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 [1957 1957 1957 3555 3555 0 nil section nil nil nil 1957 3555 nil # nil nil #15]) (paragraph (:standard-properties [1957 1957 1957 2409 2410 1 nil planning nil nil nil nil nil nil # nil nil #18]) #("Fetch the GNU Guix binary from " 0 31 (:parent #21)) (link (:standard-properties [1988 nil 2035 2039 2042 1 nil nil nil nil nil nil nil nil # nil nil #21] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/download/" :format bracket :raw-link "https://www.gnu.org/software/guix/download/" :application nil :search-option nil) #("here" 0 4 (:parent #25))) #("(middle panel) and follow\n" 0 26 (:parent #21)) (link (:standard-properties [2068 nil 2147 2159 2161 0 nil nil nil nil nil nil nil nil # nil nil #21] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :format bracket :raw-link "https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :application nil :search-option nil) #("instructions" 0 12 (:parent #27))) #(". Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #21))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("Once you have succeeded, you have to " 0 37 (:parent #22)) (link (:standard-properties [2447 nil 2523 2534 2537 1 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/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #26))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #22))) (src-block (:standard-properties [2688 2688 nil nil 2796 1 nil nil nil nil nil nil nil nil # nil nil #18] :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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("Which should show something like\n" 0 33 (:parent #24))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #18] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) (paragraph (:standard-properties [2940 2940 2940 2950 2951 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("#+end" 0 5 (:parent #26)) (subscript (:standard-properties [2945 nil 2946 2949 2949 0 nil nil nil nil nil nil nil nil # nil nil #26] :use-brackets-p nil) #("src" 0 3 (:parent #30))) #("\n" 0 1 (:parent #26))) (paragraph (:standard-properties [2951 2951 2951 3021 3022 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("means binary installs. The actual installation command of 'hello' is\n" 0 70 (:parent #27))) (src-block (:standard-properties [3022 3022 nil nil 3094 1 nil nil nil nil nil nil nil nil # nil nil #18] :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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #29))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("If you need more help we have another writeup in " 0 49 (:parent #30)) (link (:standard-properties [3330 nil 3414 3424 3426 0 nil nil nil nil nil nil nil nil # nil nil #30] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #34))) #(". To get\nrid of the locale warning see " 0 39 (:parent #30)) (link (:standard-properties [3465 nil 3540 3550 3552 0 nil nil nil nil nil nil nil nil # nil nil #30] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #36))) #(".\n" 0 2 (:parent #30))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (: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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #16]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #19]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #22))) (src-block (:standard-properties [3721 3721 nil nil 3826 1 nil nil nil nil nil nil nil nil # nil nil #19] :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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #19]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #24))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #19]) #("#+begin" 0 7 (:parent #25)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #25] :use-brackets-p nil) #("src" 0 3 (:parent #29))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #25)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #25] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #25)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #25] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #25)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #25] :use-brackets-p nil) #("src" 0 3 (:parent #35))) #("bash\n" 0 5 (:parent #25))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #19]) #("To test whether this is working try:\n" 0 37 (:parent #26))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #19]) #("#+begin" 0 7 (:parent #27)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("src" 0 3 (:parent #31))) #("bash\n#+end" 0 10 (:parent #27)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("src" 0 3 (:parent #33))) #("bash\n" 0 5 (:parent #27))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #17]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #20]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #23))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #20] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("by pasting it into the command\n" 0 31 (:parent #25))) (src-block (:standard-properties [4526 4526 nil nil 4579 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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("and hit Ctrl-D.\n" 0 16 (:parent #27))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #20]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #28))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 0 27 (: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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #18]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #21]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #24))) (src-block (:standard-properties [4832 4832 nil nil 4951 1 nil nil nil nil nil nil nil nil # nil nil #21] :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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #26))) (src-block (:standard-properties [5004 5004 nil nil 5194 1 nil nil nil nil nil nil nil nil # nil nil #21] :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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #28)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #28]) #("root" 0 4 (:parent #32))) #(".config/guix/latest override).\n" 0 31 (:parent #28))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("And install with\n" 0 17 (:parent #29))) (src-block (:standard-properties [5321 5321 nil nil 5491 1 nil nil nil nil nil nil nil nil # nil nil #21] :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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #31))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #32))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #33))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #21] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #35))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #21] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #37)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #37))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #38)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #12]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #15]) #("GNU Guix allows for " 0 20 (:parent #18)) (link (:standard-properties [6584 nil 6653 6676 6679 1 nil nil nil nil nil nil nil nil # nil nil #18] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #22))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #18))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #15] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # nil nil #15]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #20)) (link (:standard-properties [7007 nil 7112 7122 7124 0 nil nil nil nil nil nil nil nil # nil nil #20] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #24))) #(".\n" 0 2 (:parent #20))) (paragraph (:standard-properties [7127 7127 7127 7190 7191 1 nil nil nil nil nil nil nil nil # nil nil #15]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #21))) (fixed-width (:standard-properties [7191 7191 nil nil 7247 2 nil nil nil nil nil nil nil nil # nil nil #15] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [7247 7247 7247 7250 7251 1 nil nil nil nil nil nil nil nil # 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In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #9)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #13))) #("and the main " 0 13 (:parent #9)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #9] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #9))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil (org-data (:standard-properties [1 1 1 13393 13393 0 nil org-data nil nil nil 3 13393 nil # nil nil nil] :path nil :CATEGORY nil) . #0)] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (:parent #4))) :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 [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #4] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (:parent #7))) :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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #7]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #10]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #13))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #10]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. 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Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #14))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #11]) #("Once you have succeeded, you have to " 0 37 (:parent #15)) (link (:standard-properties [2447 nil 2523 2534 2537 1 nil nil nil nil nil nil nil nil # nil nil #15] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #19))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #15))) (src-block (:standard-properties [2688 2688 nil nil 2796 1 nil nil nil nil nil nil nil nil # nil nil #11] :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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #11]) #("Which should show something like\n" 0 33 (:parent #17))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #11] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) 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The actual installation command of 'hello' is\n" 0 70 (:parent #20))) (src-block (:standard-properties [3022 3022 nil nil 3094 1 nil nil nil nil nil nil nil nil # nil nil #11] :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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #11]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #22))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #11]) #("If you need more help we have another writeup in " 0 49 (:parent #23)) (link (:standard-properties [3330 nil 3414 3424 3426 0 nil nil nil nil nil nil nil nil # nil nil #23] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #27))) #(". To get\nrid of the locale warning see " 0 39 (:parent #23)) (link (:standard-properties [3465 nil 3540 3550 3552 0 nil nil nil nil nil nil nil nil # nil nil #23] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #29))) #(".\n" 0 2 (:parent #23))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #4] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (:parent #9))) :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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #9]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #12]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #15))) (src-block (:standard-properties [3721 3721 nil nil 3826 1 nil nil nil nil nil nil nil nil # nil nil #12] :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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #12]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #17))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #12]) #("#+begin" 0 7 (:parent #18)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #18] :use-brackets-p nil) #("src" 0 3 (:parent #22))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #18)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #18] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #18)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #18] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #18)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #18] :use-brackets-p nil) #("src" 0 3 (:parent #28))) #("bash\n" 0 5 (:parent #18))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #12]) #("To test whether this is working try:\n" 0 37 (:parent #19))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #12]) #("#+begin" 0 7 (:parent #20)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #20] :use-brackets-p nil) #("src" 0 3 (:parent #24))) #("bash\n#+end" 0 10 (:parent #20)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #20] :use-brackets-p nil) #("src" 0 3 (:parent #26))) #("bash\n" 0 5 (:parent #20))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #4] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (:parent #10))) :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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #10]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #13]) #("GN2 has its own GNU Guix binary distribution server. 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The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #25))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #14]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #26))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #14] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #14]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #28))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #14] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #14]) #("It will complain that the database is missing. 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These settings may\nnot reflect your system. To override settings create your own from a copy of\ndefault" 0 105 (:parent #22)) (subscript (:standard-properties [9068 nil 9069 9080 9081 1 nil nil nil nil nil nil nil nil # nil nil #22] :use-brackets-p nil) #("settings.py" 0 11 (:parent #30))) #("and pass it into GN2 with\n" 0 26 (:parent #22))) (fixed-width (:standard-properties [9108 9108 nil nil 9151 2 nil nil nil nil nil nil nil nil # nil nil #14] :value "./bin/genenetwork2 $HOME/my_settings.py")) (paragraph (:standard-properties [9151 9151 9151 9296 9297 1 nil nil nil nil nil nil nil nil # nil nil #14]) #("and everything " 0 15 (:parent #24)) (bold (:standard-properties [9166 nil 9167 9173 9175 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("should" 0 6 (:parent #28))) #("work (note the full path to the settings\nfile). 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A configuration file for\nGeneNetwork (reverse proxy) port forwarding can be found in the source\nrepository under ./etc/nginx-genenetwork.conf. Copy this file to /etc\n(still as root)\n" 0 226 (:parent #28))) (fixed-width (:standard-properties [11404 11404 nil nil 11451 2 nil nil nil nil nil nil nil nil # nil nil #15] :value "cp ./etc/nginx-genenetwork.conf /etc/nginx/")) (paragraph (:standard-properties [11451 11451 11451 11461 11462 1 nil nil nil nil nil nil nil nil # nil nil #15]) #("Make dirs\n" 0 10 (:parent #30))) (fixed-width (:standard-properties [11462 11462 nil nil 11496 2 nil nil nil nil nil nil nil nil # nil nil #15] :value "mkdir -p /var/spool/nginx/logs")) (paragraph (:standard-properties [11496 11496 11496 11506 11507 1 nil nil nil nil nil nil nil nil # nil nil #15]) #("Add users\n" 0 10 (:parent #32))) (fixed-width (:standard-properties [11507 11507 nil nil 11543 2 nil nil nil nil nil nil nil nil # nil nil #15] :value "adduser nobody ; addgroup nobody")) (paragraph (:standard-properties [11543 11543 11543 11553 11554 1 nil nil nil nil nil nil nil nil # nil nil #15]) #("Run nginx\n" 0 10 (:parent #34))) (fixed-width (:standard-properties [11554 11554 nil nil 11645 2 nil nil nil nil nil nil nil nil # nil nil #15] :value "/root/.guix-profile/sbin/nginx -c /etc/nginx/nginx-genenetwork.conf -p /var/spool/nginx"))))) (headline (:standard-properties [11645 11645 11707 13393 13393 0 (:title) nil nil nil nil 11709 13391 1 # nil nil (org-data (:standard-properties [1 1 1 13393 13393 0 nil org-data nil nil nil 3 13393 nil # nil nil nil] :path nil :CATEGORY nil) . #0)] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 60) t] :title (#("Source deployment and other information on reproducibility" 0 58 (: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 [11707 11707 11707 11764 11764 0 nil section nil nil nil 11707 11764 nil # nil nil #8]) (paragraph (:standard-properties [11707 11707 11707 11763 11764 1 nil planning nil nil nil nil nil nil # nil nil #11]) #("See the document " 0 17 (:parent #14)) (link (:standard-properties [11724 nil nil nil 11761 0 nil nil nil nil nil nil nil nil # nil nil #14] :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)) #(".\n" 0 2 (:parent #14)))) (headline (:standard-properties [11764 11764 11790 12214 12214 0 (:title) nil nil nil nil 11792 12212 2 # nil nil #8] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 24) t] :title (#("Update to recent guix" 0 21 (:parent #12))) :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 [11790 11790 11790 12214 12214 0 nil section nil nil nil 11790 12214 nil # nil nil #12]) (paragraph (:standard-properties [11790 11790 11790 11824 11825 1 nil planning nil nil nil nil nil nil # nil nil #15]) #("We now compile Guix from scratch.\n" 0 34 (:parent #18))) (paragraph (:standard-properties [11825 11825 11825 12099 12100 1 nil nil nil nil nil nil nil nil # nil nil #15]) #("Create, install and run a recent version of the guix-daemon by\ncompiling the guix repository you have installed with git in\nstep 2. 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In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #11)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #15))) #("and the main " 0 13 (:parent #11)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #11] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #11))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #0] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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) (headline (:standard-properties [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #6] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (:parent #9))) :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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #9]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #12]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #15))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #12]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. If you use a virtual machine we recommend to use at least\ndouble.\n" 0 141 (:parent #16))))) (headline (:standard-properties [1928 1928 1957 3555 3555 0 (:title) nil nil nil nil 1959 3553 2 # nil nil #6] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 27) t] :title (#("Step 1: Install GNU Guix" 0 24 (:parent #10))) :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 [1957 1957 1957 3555 3555 0 nil section nil nil nil 1957 3555 nil # nil nil #10]) (paragraph (:standard-properties [1957 1957 1957 2409 2410 1 nil planning nil nil nil nil nil nil # nil nil #13]) #("Fetch the GNU Guix binary from " 0 31 (:parent #16)) (link (:standard-properties [1988 nil 2035 2039 2042 1 nil nil nil nil nil nil nil nil # nil nil #16] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/download/" :format bracket :raw-link "https://www.gnu.org/software/guix/download/" :application nil :search-option nil) #("here" 0 4 (:parent #20))) #("(middle panel) and follow\n" 0 26 (:parent #16)) (link (:standard-properties [2068 nil 2147 2159 2161 0 nil nil nil nil nil nil nil nil # nil nil #16] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :format bracket :raw-link "https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :application nil :search-option nil) #("instructions" 0 12 (:parent #22))) #(". Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #16))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #13]) #("Once you have succeeded, you have to " 0 37 (:parent #17)) (link (:standard-properties [2447 nil 2523 2534 2537 1 nil nil nil nil nil nil nil nil # nil nil #17] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #21))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #17))) (src-block (:standard-properties [2688 2688 nil nil 2796 1 nil nil nil nil nil nil nil nil # nil nil #13] :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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #13]) #("Which should show something like\n" 0 33 (:parent #19))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #13] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) (paragraph (:standard-properties [2940 2940 2940 2950 2951 1 nil nil nil nil nil nil nil nil # nil nil #13]) #("#+end" 0 5 (:parent #21)) (subscript (:standard-properties [2945 nil 2946 2949 2949 0 nil nil nil nil nil nil nil nil # nil nil #21] :use-brackets-p nil) #("src" 0 3 (:parent #25))) #("\n" 0 1 (:parent #21))) (paragraph (:standard-properties [2951 2951 2951 3021 3022 1 nil nil nil nil nil nil nil nil # nil nil #13]) #("means binary installs. The actual installation command of 'hello' is\n" 0 70 (:parent #22))) (src-block (:standard-properties [3022 3022 nil nil 3094 1 nil nil nil nil nil nil nil nil # nil nil #13] :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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #13]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #24))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #13]) #("If you need more help we have another writeup in " 0 49 (:parent #25)) (link (:standard-properties [3330 nil 3414 3424 3426 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/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #29))) #(". To get\nrid of the locale warning see " 0 39 (:parent #25)) (link (:standard-properties [3465 nil 3540 3550 3552 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/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #31))) #(".\n" 0 2 (:parent #25))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #6] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (:parent #11))) :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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #11]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #14]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #17))) (src-block (:standard-properties [3721 3721 nil nil 3826 1 nil nil nil nil nil nil nil nil # nil nil #14] :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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #14]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #19))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #14]) #("#+begin" 0 7 (:parent #20)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #20] :use-brackets-p nil) #("src" 0 3 (:parent #24))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #20)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #20] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #20)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #20] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #20)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #20] :use-brackets-p nil) #("src" 0 3 (:parent #30))) #("bash\n" 0 5 (:parent #20))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #14]) #("To test whether this is working try:\n" 0 37 (:parent #21))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #14]) #("#+begin" 0 7 (:parent #22)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #22] :use-brackets-p nil) #("src" 0 3 (:parent #26))) #("bash\n#+end" 0 10 (:parent #22)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #22] :use-brackets-p nil) #("src" 0 3 (:parent #28))) #("bash\n" 0 5 (:parent #22))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #6] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (:parent #12))) :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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #12]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #15]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #18))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #15] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #15]) #("by pasting it into the command\n" 0 31 (:parent #20))) (src-block (:standard-properties [4526 4526 nil nil 4579 1 nil nil nil nil nil nil nil nil # nil nil #15] :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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #15]) #("and hit Ctrl-D.\n" 0 16 (:parent #22))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #15]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #23))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #6] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 0 27 (:parent #13))) :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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #13]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #16]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #19))) (src-block (:standard-properties [4832 4832 nil nil 4951 1 nil nil nil nil nil nil nil nil # nil nil #16] :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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #21))) (src-block (:standard-properties [5004 5004 nil nil 5194 1 nil nil nil nil nil nil nil nil # nil nil #16] :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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #23)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #23]) #("root" 0 4 (:parent #27))) #(".config/guix/latest override).\n" 0 31 (:parent #23))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("And install with\n" 0 17 (:parent #24))) (src-block (:standard-properties [5321 5321 nil nil 5491 1 nil nil nil nil nil nil nil nil # nil nil #16] :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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #26))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #27))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #28))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #16] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #30))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #16] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #32)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #32))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #33)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #0] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #7]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #10]) #("GNU Guix allows for " 0 20 (:parent #13)) (link (:standard-properties [6584 nil 6653 6676 6679 1 nil nil nil nil nil nil nil nil # nil nil #13] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #17))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #13))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #10] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # nil nil #10]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #15)) (link (:standard-properties [7007 nil 7112 7122 7124 0 nil nil nil nil nil nil nil nil # nil nil #15] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #19))) #(".\n" 0 2 (:parent #15))) (paragraph (:standard-properties [7127 7127 7127 7190 7191 1 nil nil nil nil nil nil nil nil # nil nil #10]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #16))) (fixed-width (:standard-properties [7191 7191 nil nil 7247 2 nil nil nil nil nil nil nil nil # nil nil #10] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [7247 7247 7247 7250 7251 1 nil nil nil nil nil nil nil nil # 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nil nil #352]) #("Large system deployments tend to get very complex. In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #355)) (link (:standard-properties [1299 nil 1361 1371 1374 1 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 #359))) #("and the main " 0 13 (:parent #355)) (link (:standard-properties [1387 nil nil nil 1402 1 nil nil nil nil nil nil nil nil # nil nil #355] :type "fuzzy" :type-explicit-p nil :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil)) #("doc).\n" 0 6 (:parent #355))))) (headline (:standard-properties [1409 1409 1446 6538 6538 0 (:title) nil nil nil nil 1448 6536 1 # nil nil #344] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 36) t] :title (#("Binary deployment through GNU Guix" 0 34 (: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) (headline (:standard-properties [1446 1446 1476 1928 1928 0 (:title) section nil nil nil 1478 1926 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 28) t] :title (#("Quick installation recipe" 0 25 (:parent #353))) :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 [1476 1476 1476 1928 1928 0 nil section nil nil nil 1476 1928 nil # nil nil #353]) (paragraph (:standard-properties [1476 1476 1476 1784 1786 2 nil planning nil nil nil nil nil nil # nil nil #356]) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #359))) (paragraph (:standard-properties [1786 1786 1786 1927 1928 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. If you use a virtual machine we recommend to use at least\ndouble.\n" 0 141 (:parent #360))))) (headline (:standard-properties [1928 1928 1957 3555 3555 0 (:title) nil nil nil nil 1959 3553 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 27) t] :title (#("Step 1: Install GNU Guix" 0 24 (:parent #354))) :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 [1957 1957 1957 3555 3555 0 nil section nil nil nil 1957 3555 nil # nil nil #354]) (paragraph (:standard-properties [1957 1957 1957 2409 2410 1 nil planning nil nil nil nil nil nil # nil nil #357]) #("Fetch the GNU Guix binary from " 0 31 (:parent #360)) (link (:standard-properties [1988 nil 2035 2039 2042 1 nil nil nil nil nil nil nil nil # nil nil #360] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/download/" :format bracket :raw-link "https://www.gnu.org/software/guix/download/" :application nil :search-option nil) #("here" 0 4 (:parent #364))) #("(middle panel) and follow\n" 0 26 (:parent #360)) (link (:standard-properties [2068 nil 2147 2159 2161 0 nil nil nil nil nil nil nil nil # nil nil #360] :type "https" :type-explicit-p t :path "//www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :format bracket :raw-link "https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :application nil :search-option nil) #("instructions" 0 12 (:parent #366))) #(". Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #360))) (paragraph (:standard-properties [2410 2410 2410 2687 2688 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("Once you have succeeded, you have to " 0 37 (:parent #361)) (link (:standard-properties [2447 nil 2523 2534 2537 1 nil nil nil nil nil nil nil nil # nil nil #361] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil) #("set the key" 0 11 (:parent #365))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #361))) (src-block (:standard-properties [2688 2688 nil nil 2796 1 nil nil nil nil nil nil nil nil # nil nil #357] :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 97) t])) (paragraph (:standard-properties [2796 2796 2796 2829 2830 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("Which should show something like\n" 0 33 (:parent #363))) (fixed-width (:standard-properties [2830 2830 nil nil 2940 1 nil nil nil nil nil nil nil nil # nil nil #357] :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ...")) (paragraph (:standard-properties [2940 2940 2940 2950 2951 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("#+end" 0 5 (:parent #365)) (subscript (:standard-properties [2945 nil 2946 2949 2949 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("src" 0 3 (:parent #369))) #("\n" 0 1 (:parent #365))) (paragraph (:standard-properties [2951 2951 2951 3021 3022 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("means binary installs. The actual installation command of 'hello' is\n" 0 70 (:parent #366))) (src-block (:standard-properties [3022 3022 nil nil 3094 1 nil nil nil nil nil nil nil nil # nil nil #357] :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 61) t])) (paragraph (:standard-properties [3094 3094 3094 3280 3281 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #368))) (paragraph (:standard-properties [3281 3281 3281 3554 3555 1 nil nil nil nil nil nil nil nil # nil nil #357]) #("If you need more help we have another writeup in " 0 49 (:parent #369)) (link (:standard-properties [3330 nil 3414 3424 3426 0 nil nil nil nil nil nil nil nil # nil nil #369] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #373))) #(". To get\nrid of the locale warning see " 0 39 (:parent #369)) (link (:standard-properties [3465 nil 3540 3550 3552 0 nil nil nil nil nil nil nil nil # nil nil #369] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil) #("set-locale" 0 10 (:parent #375))) #(".\n" 0 2 (:parent #369))))) (headline (:standard-properties [3555 3555 3601 4209 4209 0 (:title) nil nil nil nil 3603 4207 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 44) t] :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (:parent #355))) :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 [3601 3601 3601 4209 4209 0 nil section nil nil nil 3601 4209 nil # nil nil #355]) (paragraph (:standard-properties [3601 3601 3601 3720 3721 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #361))) (src-block (:standard-properties [3721 3721 nil nil 3826 1 nil nil nil nil nil nil nil nil # nil nil #358] :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 94) t])) (paragraph (:standard-properties [3826 3826 3826 3876 3877 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #363))) (paragraph (:standard-properties [3877 3877 3877 4137 4138 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("#+begin" 0 7 (:parent #364)) (subscript (:standard-properties [3884 nil 3885 3888 3889 1 nil nil nil nil nil nil nil nil # nil nil #364] :use-brackets-p nil) #("src" 0 3 (:parent #368))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #364)) (link (:standard-properties [3961 nil nil nil 4011 0 nil nil nil nil nil nil nil nil # nil nil #364] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #364)) (link (:standard-properties [4053 nil nil nil 4089 1 nil nil nil nil nil nil nil nil # nil nil #364] :type "https" :type-explicit-p t :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #364)) (subscript (:standard-properties [4127 nil 4128 4131 4132 1 nil nil nil nil nil nil nil nil # nil nil #364] :use-brackets-p nil) #("src" 0 3 (:parent #374))) #("bash\n" 0 5 (:parent #364))) (paragraph (:standard-properties [4138 4138 4138 4175 4176 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("To test whether this is working try:\n" 0 37 (:parent #365))) (paragraph (:standard-properties [4176 4176 4176 4208 4209 1 nil nil nil nil nil nil nil nil # nil nil #358]) #("#+begin" 0 7 (:parent #366)) (subscript (:standard-properties [4183 nil 4184 4187 4188 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("src" 0 3 (:parent #370))) #("bash\n#+end" 0 10 (:parent #366)) (subscript (:standard-properties [4198 nil 4199 4202 4203 1 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("src" 0 3 (:parent #372))) #("bash\n" 0 5 (:parent #366))))) (headline (:standard-properties [4209 4209 4250 4660 4660 0 (:title) nil nil nil nil 4252 4658 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 39) t] :title (#("Step 3: Authorize the GN Guix server" 0 36 (: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 [4250 4250 4250 4660 4660 0 nil section nil nil nil 4250 4660 nil # nil nil #356]) (paragraph (:standard-properties [4250 4250 4250 4349 4350 1 nil planning nil nil nil nil nil nil # nil nil #359]) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #362))) (src-block (:standard-properties [4350 4350 nil nil 4494 1 nil nil nil nil nil nil nil nil # nil nil #359] :language "scheme" :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 (19 133) t])) (paragraph (:standard-properties [4494 4494 4494 4525 4526 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("by pasting it into the command\n" 0 31 (:parent #364))) (src-block (:standard-properties [4526 4526 nil nil 4579 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 42) t])) (paragraph (:standard-properties [4579 4579 4579 4595 4596 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("and hit Ctrl-D.\n" 0 16 (:parent #366))) (paragraph (:standard-properties [4596 4596 4596 4659 4660 1 nil nil nil nil nil nil nil nil # nil nil #359]) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #367))))) (headline (:standard-properties [4660 4660 4692 6538 6538 0 (:title) nil nil nil nil 4694 6536 2 # nil nil #350] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Step 4: Install and run GN2" 0 27 (: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 [4692 4692 4692 6538 6538 0 nil section nil nil nil 4692 6538 nil # nil nil #357]) (paragraph (:standard-properties [4692 4692 4692 4831 4832 1 nil planning nil nil nil nil nil nil # nil nil #360]) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #363))) (src-block (:standard-properties [4832 4832 nil nil 4951 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 108) t])) (paragraph (:standard-properties [4951 4951 4951 5003 5004 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #365))) (src-block (:standard-properties [5004 5004 nil nil 5194 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 179) t])) (paragraph (:standard-properties [5194 5194 5194 5302 5303 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #367)) (italic (:standard-properties [5265 nil 5266 5270 5271 0 nil nil nil nil nil nil nil nil # nil nil #367]) #("root" 0 4 (:parent #371))) #(".config/guix/latest override).\n" 0 31 (:parent #367))) (paragraph (:standard-properties [5303 5303 5303 5320 5321 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("And install with\n" 0 17 (:parent #368))) (src-block (:standard-properties [5321 5321 nil nil 5491 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 159) t])) (paragraph (:standard-properties [5491 5491 5491 5633 5634 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #370))) (paragraph (:standard-properties [5634 5634 5634 5829 5830 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #371))) (paragraph (:standard-properties [5830 5830 5830 5960 5961 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #372))) (src-block (:standard-properties [5961 5961 nil nil 6140 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 (17 168) t])) (paragraph (:standard-properties [6140 6140 6140 6208 6209 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #374))) (src-block (:standard-properties [6209 6209 nil nil 6250 1 nil nil nil nil nil nil nil nil # nil nil #360] :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 30) t])) (paragraph (:standard-properties [6250 6250 6250 6500 6501 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #376)) (link (:standard-properties [6472 nil nil nil 6498 0 nil nil nil nil nil nil nil nil # nil nil #376] :type "http" :type-explicit-p t :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil)) #(".\n" 0 2 (:parent #376))) (paragraph (:standard-properties [6501 6501 6501 6537 6538 1 nil nil nil nil nil nil nil nil # nil nil #360]) #("End of the GN2 installation recipe!\n" 0 36 (:parent #377)))))) (headline (:standard-properties [6538 6538 6564 7812 7812 0 (:title) nil nil nil nil 6566 7810 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (: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 [6564 6564 6564 7812 7812 0 nil section nil nil nil 6564 7812 nil # nil nil #351]) (paragraph (:standard-properties [6564 6564 6564 6744 6745 1 nil planning nil nil nil nil nil nil # nil nil #354]) #("GNU Guix allows for " 0 20 (:parent #357)) (link (:standard-properties [6584 nil 6653 6676 6679 1 nil nil nil nil nil nil nil nil # nil nil #357] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #361))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #357))) (src-block (:standard-properties [6745 6745 nil nil 6951 1 nil nil nil nil nil nil nil nil # nil nil #354] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [6951 6951 6951 7126 7127 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #359)) (link (:standard-properties [7007 nil 7112 7122 7124 0 nil nil nil nil nil nil nil nil # nil nil #359] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #363))) #(".\n" 0 2 (:parent #359))) (paragraph (:standard-properties [7127 7127 7127 7190 7191 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #360))) (fixed-width (:standard-properties [7191 7191 nil nil 7247 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [7247 7247 7247 7250 7251 1 nil nil nil nil nil nil nil nil # 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