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Error: user-error ("Unable to resolve link: \"introduction\"") mapbacktrace(#f(compiled-function (evald func args flags) #)) debug-early-backtrace() debug-early(error (user-error "Unable to resolve link: \"introduction\"")) signal(user-error ("Unable to resolve link: \"introduction\"")) user-error("Unable to resolve link: %S" "introduction") org-export-data((link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 125 :end 156 :contents-begin 142 :contents-end 154 :post-blank 0 :parent (paragraph (:begin 125 :end 157 :contents-begin 125 :contents-end 157 :post-blank 0 :post-affiliated 125 :mode nil :granularity nil :parent (item (:bullet "- " :begin 122 :end 157 :contents-begin 125 :contents-end 157 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 122 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 122 :end 980 :contents-begin 122 :contents-end 980 :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :post-blank 0 :post-affiliated 122 :mode planning :granularity nil :parent (section (:begin 122 :end 981 :contents-begin 122 :contents-end 980 :robust-begin 122 :robust-end 978 :post-blank 1 :post-affiliated 122 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 44 :end 981 :pre-blank 0 :contents-begin 122 :contents-end 980 :robust-begin 124 :robust-end 978 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 44 :title (#("Table of Contents" 0 17 (:parent #126))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 2 :contents-end 17451 :end 17451 :robust-begin 4 :robust-end 17449 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 2 :end 44 :contents-begin 2 :contents-end 43 :robust-begin 2 :robust-end 41 :post-blank 1 :post-affiliated 2 :mode first-section :granularity nil :parent #172) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 2 :end 43 :post-blank 0 :post-affiliated 2 :mode top-comment :granularity nil :parent #175))) #126 (headline (:raw-value "Introduction" :begin 981 :end 1722 :pre-blank 1 :contents-begin 997 :contents-end 1721 :robust-begin 999 :robust-end 1719 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #177))) :mode nil :granularity nil :parent #172) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #177) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #180) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #183)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #183) #("Guix-notes" 0 10 (:parent #187))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #183))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #180) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #184)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #184) #("Guix bioinformatics" 0 19 (:parent #188))) #("and " 0 4 (:parent #184)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #184) #("GNU Guix main" 0 13 (:parent #190))) #(".\n" 0 2 (:parent #184))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #178))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #181))) :mode section :granularity nil :parent #178) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #181) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #184) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #187)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #187) #("here" 0 4 (:parent #191))) #(".\n" 0 2 (:parent #187))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #184) #("If it works you should be able to install a package with\n" 0 57 (:parent #188))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #184)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #182))) :mode nil :granularity nil :parent #178) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #182) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #185) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #188))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #185) #("#+begin" 0 7 (:parent #189)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #189) #("src" 0 3 (:parent #193))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #189)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #189)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #189)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #189)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #189)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #189) #("src" 0 3 (:parent #199))) #("bash\n" 0 5 (:parent #189))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #183))) :mode nil :granularity nil :parent #178) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #183) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #186) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #189)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #189) #("these" 0 5 (:parent #193))) #("steps carefully.\n" 0 17 (:parent #189))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #184))) :mode nil :granularity nil :parent #178) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #184) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #187) #("#+begin" 0 7 (:parent #190)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #190) #("src" 0 3 (:parent #194))) #("bash\nenv GUIX" 0 13 (:parent #190)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #190) #("PACKAGE" 0 7 (:parent #196))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #190) #("PATH" 0 4 (:parent #197))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #190)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #190) #("src" 0 3 (:parent #199))) #("bash\n" 0 5 (:parent #190))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #187) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #191)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #191)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #191))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #187) #("#+begin" 0 7 (:parent #192)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #192) #("src" 0 3 (:parent #196))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #192))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #187) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #193))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #187) #(" yes\n env GUIX" 0 30 (:parent #194)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #194) #("PACKAGE" 0 7 (:parent #198))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #194) #("PATH" 0 4 (:parent #199))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #194))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #187) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #195))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #187) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #196)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #196) #("PACKAGE" 0 7 (:parent #200))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #196) #("PATH" 0 4 (:parent #201))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #196))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #187) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #197))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #187) #(" which should have the same HASH values " 0 48 (:parent #198)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #198) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #202))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #198)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #198)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #198)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #198)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #208))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #209))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #198)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #198)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #213))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #214))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #198)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #216))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #217))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #198)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #198)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #198)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #223))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #224))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #198)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #198)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #198)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #198)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #230))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #231))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #198)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #198)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #198)))))))) #102)) #78)) #46 (item (:bullet "- " :begin 157 :end 582 :contents-begin 160 :contents-end 582 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 157 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 160 :end 202 :contents-begin 160 :contents-end 202 :post-blank 0 :post-affiliated 160 :mode nil :granularity nil :parent #82) (link (:type "custom-id" :path "source-deployment" :format bracket :raw-link "#source-deployment" :application nil :search-option nil :begin 160 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #353))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #350) #("GNU Guix main" 0 13 (:parent #356))) #(".\n" 0 2 (:parent #350))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #344))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #347))) :mode section :granularity nil :parent #344) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #347) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #350) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #353)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #353) #("here" 0 4 (:parent #357))) #(".\n" 0 2 (:parent #353))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #350) #("If it works you should be able to install a package with\n" 0 57 (:parent #354))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #350)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #348))) :mode nil :granularity nil :parent #344) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #348) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #351) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #354))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #351) #("#+begin" 0 7 (:parent #355)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #355) #("src" 0 3 (:parent #359))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #355)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #355)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #355)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #355)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #355) #("src" 0 3 (:parent #365))) #("bash\n" 0 5 (:parent #355))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #349))) :mode nil :granularity nil :parent #344) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #349) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #352) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #355)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #355) #("these" 0 5 (:parent #359))) #("steps carefully.\n" 0 17 (:parent #355))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #350))) :mode nil :granularity nil :parent #344) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #350) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #353) #("#+begin" 0 7 (:parent #356)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #356) #("src" 0 3 (:parent #360))) #("bash\nenv GUIX" 0 13 (:parent #356)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #356) #("PACKAGE" 0 7 (:parent #362))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #356) #("PATH" 0 4 (:parent #363))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #356)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #356) #("src" 0 3 (:parent #365))) #("bash\n" 0 5 (:parent #356))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #353) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #357)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #357)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #357))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #353) #("#+begin" 0 7 (:parent #358)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #358) #("src" 0 3 (:parent #362))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #358))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #353) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #359))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #353) #(" yes\n env GUIX" 0 30 (:parent #360)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #360) #("PACKAGE" 0 7 (:parent #364))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #360) #("PATH" 0 4 (:parent #365))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #360))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #353) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #361))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #353) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #362)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #362) #("PACKAGE" 0 7 (:parent #366))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #362) #("PATH" 0 4 (:parent #367))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #362))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #353) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #363))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #353) #(" which should have the same HASH values " 0 48 (:parent #364)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #364) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #368))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #364)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #374))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #375))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #364)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #364)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #379))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #380))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #364)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #382))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #383))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #364)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #389))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #390))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #364)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #364)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #396))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #397))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #364))))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 125 :end 156 :contents-begin 142 :contents-end 154 :post-blank 0 :parent (paragraph (:begin 125 :end 157 :contents-begin 125 :contents-end 157 :post-blank 0 :post-affiliated 125 :mode nil :granularity nil :parent (item (:bullet "- " :begin 122 :end 157 :contents-begin 125 :contents-end 157 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 122 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 122 :end 980 :contents-begin 122 :contents-end 980 :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :post-blank 0 :post-affiliated 122 :mode planning :granularity nil :parent (section (:begin 122 :end 981 :contents-begin 122 :contents-end 980 :robust-begin 122 :robust-end 978 :post-blank 1 :post-affiliated 122 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 44 :end 981 :pre-blank 0 :contents-begin 122 :contents-end 980 :robust-begin 124 :robust-end 978 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 44 :title (#("Table of Contents" 0 17 (:parent #126))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 2 :contents-end 17451 :end 17451 :robust-begin 4 :robust-end 17449 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 2 :end 44 :contents-begin 2 :contents-end 43 :robust-begin 2 :robust-end 41 :post-blank 1 :post-affiliated 2 :mode first-section :granularity nil :parent #172) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 2 :end 43 :post-blank 0 :post-affiliated 2 :mode top-comment :granularity nil :parent #175))) #126 (headline (:raw-value "Introduction" :begin 981 :end 1722 :pre-blank 1 :contents-begin 997 :contents-end 1721 :robust-begin 999 :robust-end 1719 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #177))) :mode nil :granularity nil :parent #172) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #177) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #180) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #183)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #183) #("Guix-notes" 0 10 (:parent #187))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #183))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #180) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #184)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #184) #("Guix bioinformatics" 0 19 (:parent #188))) #("and " 0 4 (:parent #184)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #184) #("GNU Guix main" 0 13 (:parent #190))) #(".\n" 0 2 (:parent #184))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #178))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #181))) :mode section :granularity nil :parent #178) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #181) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #184) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #187)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #187) #("here" 0 4 (:parent #191))) #(".\n" 0 2 (:parent #187))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #184) #("If it works you should be able to install a package with\n" 0 57 (:parent #188))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #184)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #182))) :mode nil :granularity nil :parent #178) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #182) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #185) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #188))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #185) #("#+begin" 0 7 (:parent #189)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #189) #("src" 0 3 (:parent #193))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #189)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #189)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #189)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #189)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #189)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #189) #("src" 0 3 (:parent #199))) #("bash\n" 0 5 (:parent #189))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #183))) :mode nil :granularity nil :parent #178) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #183) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #186) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #189)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #189) #("these" 0 5 (:parent #193))) #("steps carefully.\n" 0 17 (:parent #189))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #184))) :mode nil :granularity nil :parent #178) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #184) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #187) #("#+begin" 0 7 (:parent #190)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #190) #("src" 0 3 (:parent #194))) #("bash\nenv GUIX" 0 13 (:parent #190)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #190) #("PACKAGE" 0 7 (:parent #196))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #190) #("PATH" 0 4 (:parent #197))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #190)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #190) #("src" 0 3 (:parent #199))) #("bash\n" 0 5 (:parent #190))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #187) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #191)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #191)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #191))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #187) #("#+begin" 0 7 (:parent #192)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #192) #("src" 0 3 (:parent #196))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #192))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #187) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #193))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #187) #(" yes\n env GUIX" 0 30 (:parent #194)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #194) #("PACKAGE" 0 7 (:parent #198))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #194) #("PATH" 0 4 (:parent #199))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #194))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #187) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #195))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #187) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #196)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #196) #("PACKAGE" 0 7 (:parent #200))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #196) #("PATH" 0 4 (:parent #201))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #196))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #187) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #197))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #187) #(" which should have the same HASH values " 0 48 (:parent #198)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #198) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #202))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #198)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #198)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #198)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #198)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #208))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #209))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #198)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #198)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #213))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #214))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #198)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #216))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #217))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #198)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #198)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #198)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #223))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #224))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #198)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #198)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #198)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #198)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #230))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #231))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #198)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #198)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #198)))))))) #102)) #78)) #46 (item (:bullet "- " :begin 157 :end 582 :contents-begin 160 :contents-end 582 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 157 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 160 :end 202 :contents-begin 160 :contents-end 202 :post-blank 0 :post-affiliated 160 :mode nil :granularity nil :parent #82) (link (:type "custom-id" :path "source-deployment" :format bracket :raw-link "#source-deployment" :application nil :search-option nil :begin 160 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:tag nil :mode item :granularity nil :parent #88) (paragraph (:begin 757 :end 834 :contents-begin 757 :contents-end 834 :post-blank 0 :post-affiliated 757 :mode nil :granularity nil :parent #91) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 757 :end 833 :contents-begin 796 :contents-end 831 :post-blank 0 :parent #94) #("ImportError: No module named jinja2" 0 35 (:parent #97))) #("\n" 0 1 (:parent #94)))) (item (:bullet "- " :begin 834 :end 932 :contents-begin 839 :contents-end 932 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 834 :tag nil :mode item :granularity nil :parent #88) (paragraph (:begin 839 :end 932 :contents-begin 839 :contents-end 932 :post-blank 0 :post-affiliated 839 :mode nil :granularity nil :parent #92) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data" :application nil :search-option nil :begin 839 :end 931 :contents-begin 885 :contents-end 929 :post-blank 0 :parent #95) #("ERROR: can not find directory $HOME/gn2" 0 39 (:parent #98)) (subscript (:begin 924 :end 929 :use-brackets-p nil :contents-begin 925 :contents-end 929 :post-blank 0 :parent #98) #("data" 0 4 (:parent #102)))) #("\n" 0 1 (:parent #95)))) (item (:bullet "- " :begin 932 :end 980 :contents-begin 937 :contents-end 980 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 932 :tag nil :mode item :granularity nil :parent #88) (paragraph (:begin 937 :end 980 :contents-begin 937 :contents-end 980 :post-blank 0 :post-affiliated 937 :mode nil :granularity nil :parent #93) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 937 :end 979 :contents-begin 959 :contents-end 977 :post-blank 0 :parent #96) #("Can't run a module" 0 18 (:parent #99))) #("\n" 0 1 (:parent #96)))))))) #26)) #0 #("\n" 0 1 (:parent #26)))) #("Introduction" 0 12 (:parent #0)))) mapconcat(#f(compiled-function (element) #) ((link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 125 :end 156 :contents-begin 142 :contents-end 154 :post-blank 0 :parent (paragraph (:begin 125 :end 157 :contents-begin 125 :contents-end 157 :post-blank 0 :post-affiliated 125 :mode nil :granularity nil :parent (item (:bullet "- " :begin 122 :end 157 :contents-begin 125 :contents-end 157 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 122 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 122 :end 980 :contents-begin 122 :contents-end 980 :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :post-blank 0 :post-affiliated 122 :mode planning :granularity nil :parent (section (:begin 122 :end 981 :contents-begin 122 :contents-end 980 :robust-begin 122 :robust-end 978 :post-blank 1 :post-affiliated 122 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 44 :end 981 :pre-blank 0 :contents-begin 122 :contents-end 980 :robust-begin 124 :robust-end 978 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 44 :title (#("Table of Contents" 0 17 (:parent #127))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 2 :contents-end 17451 :end 17451 :robust-begin 4 :robust-end 17449 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 2 :end 44 :contents-begin 2 :contents-end 43 :robust-begin 2 :robust-end 41 :post-blank 1 :post-affiliated 2 :mode first-section :granularity nil :parent #173) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 2 :end 43 :post-blank 0 :post-affiliated 2 :mode top-comment :granularity nil :parent #176))) #127 (headline (:raw-value "Introduction" :begin 981 :end 1722 :pre-blank 1 :contents-begin 997 :contents-end 1721 :robust-begin 999 :robust-end 1719 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #178))) :mode nil :granularity nil :parent #173) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #178) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #181) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #184)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #184) #("Guix-notes" 0 10 (:parent #188))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #184))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #181) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #185)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #185) #("Guix bioinformatics" 0 19 (:parent #189))) #("and " 0 4 (:parent #185)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #185) #("GNU Guix main" 0 13 (:parent #191))) #(".\n" 0 2 (:parent #185))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #179))) :mode nil :granularity nil :parent #173) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #182))) :mode section :granularity nil :parent #179) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #182) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #185) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #188)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #188) #("here" 0 4 (:parent #192))) #(".\n" 0 2 (:parent #188))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #185) #("If it works you should be able to install a package with\n" 0 57 (:parent #189))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #185)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #183))) :mode nil :granularity nil :parent #179) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #183) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #186) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #189))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #186) #("#+begin" 0 7 (:parent #190)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #190) #("src" 0 3 (:parent #194))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #190)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #190)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #190)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #190)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #190)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #190) #("src" 0 3 (:parent #200))) #("bash\n" 0 5 (:parent #190))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #184))) :mode nil :granularity nil :parent #179) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #184) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #187) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #190)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #190) #("these" 0 5 (:parent #194))) #("steps carefully.\n" 0 17 (:parent #190))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #185))) :mode nil :granularity nil :parent #179) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #185) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #188) #("#+begin" 0 7 (:parent #191)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #191) #("src" 0 3 (:parent #195))) #("bash\nenv GUIX" 0 13 (:parent #191)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #191) #("PACKAGE" 0 7 (:parent #197))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #191) #("PATH" 0 4 (:parent #198))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #191)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #191) #("src" 0 3 (:parent #200))) #("bash\n" 0 5 (:parent #191))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #188) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #192)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #192)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #192))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #188) #("#+begin" 0 7 (:parent #193)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #193) #("src" 0 3 (:parent #197))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #193))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #188) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #194))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #188) #(" yes\n env GUIX" 0 30 (:parent #195)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #195) #("PACKAGE" 0 7 (:parent #199))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #195) #("PATH" 0 4 (:parent #200))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #195))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #188) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #196))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #188) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #197)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #197) #("PACKAGE" 0 7 (:parent #201))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #197) #("PATH" 0 4 (:parent #202))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #197))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #188) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #198))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #188) #(" which should have the same HASH values " 0 48 (:parent #199)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #199) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #203))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #199)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #199)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #199)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #199)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #199)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #199) #("PACKAGE" 0 7 (:parent #209))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #199) #("PATH" 0 4 (:parent #210))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #199)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #199)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #199)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #199) #("PACKAGE" 0 7 (:parent #214))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #199) #("PATH" 0 4 (:parent #215))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #199)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #199) #("PACKAGE" 0 7 (:parent #217))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #199) #("PATH" 0 4 (:parent #218))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #199)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #199)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #199)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #199)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #199)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #199) #("PACKAGE" 0 7 (:parent #224))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #199) #("PATH" 0 4 (:parent #225))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #199)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #199)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #199)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #199)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #199)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #199) #("PACKAGE" 0 7 (:parent #231))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #199) #("PATH" 0 4 (:parent #232))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #199)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #199)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #199)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #199)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #199)))))))) #103)) #79)) #47 (item (:bullet "- " :begin 157 :end 582 :contents-begin 160 :contents-end 582 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 157 :tag nil :mode item :granularity nil :parent #79) (paragraph (:begin 160 :end 202 :contents-begin 160 :contents-end 202 :post-blank 0 :post-affiliated 160 :mode nil :granularity nil :parent #83) (link (:type "custom-id" :path "source-deployment" :format bracket :raw-link "#source-deployment" :application nil :search-option nil :begin 160 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157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 932 :tag nil :mode item :granularity nil :parent #89) (paragraph (:begin 937 :end 980 :contents-begin 937 :contents-end 980 :post-blank 0 :post-affiliated 937 :mode nil :granularity nil :parent #94) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 937 :end 979 :contents-begin 959 :contents-end 977 :post-blank 0 :parent #97) #("Can't run a module" 0 18 (:parent #100))) #("\n" 0 1 (:parent #97)))))))) #27)) . #0)) #("Introduction" 0 12 (:parent #1))) #("\n" 0 1 (:parent (paragraph (:begin 125 :end 157 :contents-begin 125 :contents-end 157 :post-blank 0 :post-affiliated 125 :mode nil :granularity nil :parent (item (:bullet "- " :begin 122 :end 157 :contents-begin 125 :contents-end 157 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 122 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 122 :end 980 :contents-begin 122 :contents-end 980 :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 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:robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #156) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #159) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #162)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #162) #("Guix-notes" 0 10 (:parent #166))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #162))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #159) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #163)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #163) #("Guix bioinformatics" 0 19 (:parent #167))) #("and " 0 4 (:parent #163)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #163) #("GNU Guix main" 0 13 (:parent #169))) #(".\n" 0 2 (:parent #163))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #157))) :mode nil :granularity nil :parent #151) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #160))) :mode section :granularity nil :parent #157) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #160) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #163) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #166)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #166) #("here" 0 4 (:parent #170))) #(".\n" 0 2 (:parent #166))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #163) #("If it works you should be able to install a package with\n" 0 57 (:parent #167))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #163)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #161))) :mode nil :granularity nil :parent #157) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #161) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #164) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #167))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #164) #("#+begin" 0 7 (:parent #168)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #168) #("src" 0 3 (:parent #172))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #168)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #168)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #168)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #168)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #168)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #168) #("src" 0 3 (:parent #178))) #("bash\n" 0 5 (:parent #168))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #162))) :mode nil :granularity nil :parent #157) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #162) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #165) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #168)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #168) #("these" 0 5 (:parent #172))) #("steps carefully.\n" 0 17 (:parent #168))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #163))) :mode nil :granularity nil :parent #157) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #163) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #166) #("#+begin" 0 7 (:parent #169)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #169) #("src" 0 3 (:parent #173))) #("bash\nenv GUIX" 0 13 (:parent #169)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #169) #("PACKAGE" 0 7 (:parent #175))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #169) #("PATH" 0 4 (:parent #176))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #169)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #169) #("src" 0 3 (:parent #178))) #("bash\n" 0 5 (:parent #169))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #166) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #170)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #170)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #170))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #166) #("#+begin" 0 7 (:parent #171)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #171) #("src" 0 3 (:parent #175))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #171))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #166) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #172))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #166) #(" yes\n env GUIX" 0 30 (:parent #173)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #173) #("PACKAGE" 0 7 (:parent #177))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #173) #("PATH" 0 4 (:parent #178))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #173))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #166) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #174))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #166) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #175)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #175) #("PACKAGE" 0 7 (:parent #179))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #175) #("PATH" 0 4 (:parent #180))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #175))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #166) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #176))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #166) #(" which should have the same HASH values " 0 48 (:parent #177)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #177) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #181))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #177)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #177)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #177)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #177)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #177)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #177) #("PACKAGE" 0 7 (:parent #187))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #177) #("PATH" 0 4 (:parent #188))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #177)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #177)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #177)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #177) #("PACKAGE" 0 7 (:parent #192))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #177) #("PATH" 0 4 (:parent #193))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #177)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #177) #("PACKAGE" 0 7 (:parent #195))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #177) #("PATH" 0 4 (:parent #196))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #177)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #177)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #177)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #177)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #177)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #177) #("PACKAGE" 0 7 (:parent #202))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #177) #("PATH" 0 4 (:parent #203))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #177)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #177)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #177)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #177)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #177)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #177) #("PACKAGE" 0 7 (:parent #209))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #177) #("PATH" 0 4 (:parent #210))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #177)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #177)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #177)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #177)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow 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:post-affiliated 997 :mode section :granularity nil :parent #151) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #154) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #157)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #157) #("Guix-notes" 0 10 (:parent #161))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #157))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #154) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #158)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #158) #("Guix bioinformatics" 0 19 (:parent #162))) #("and " 0 4 (:parent #158)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #158) #("GNU Guix main" 0 13 (:parent #164))) #(".\n" 0 2 (:parent #158))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #152))) :mode nil :granularity nil :parent #146) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #155))) :mode section :granularity nil :parent #152) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #155) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #158) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #161)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #161) #("here" 0 4 (:parent #165))) #(".\n" 0 2 (:parent #161))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #158) #("If it works you should be able to install a package with\n" 0 57 (:parent #162))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #158)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #156))) :mode nil :granularity nil :parent #152) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #156) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #159) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #162))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #159) #("#+begin" 0 7 (:parent #163)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #163) #("src" 0 3 (:parent #167))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #163)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #163)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #163)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #163)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #163)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #163) #("src" 0 3 (:parent #173))) #("bash\n" 0 5 (:parent #163))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #157))) :mode nil :granularity nil :parent #152) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #157) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #160) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #163)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #163) #("these" 0 5 (:parent #167))) #("steps carefully.\n" 0 17 (:parent #163))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #158))) :mode nil :granularity nil :parent #152) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #158) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #161) #("#+begin" 0 7 (:parent #164)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #164) #("src" 0 3 (:parent #168))) #("bash\nenv GUIX" 0 13 (:parent #164)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #164) #("PACKAGE" 0 7 (:parent #170))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #164) #("PATH" 0 4 (:parent #171))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #164)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #164) #("src" 0 3 (:parent #173))) #("bash\n" 0 5 (:parent #164))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #161) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #165)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #165)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #165))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #161) #("#+begin" 0 7 (:parent #166)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #166) #("src" 0 3 (:parent #170))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #166))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #161) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #167))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #161) #(" yes\n env GUIX" 0 30 (:parent #168)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #168) #("PACKAGE" 0 7 (:parent #172))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #168) #("PATH" 0 4 (:parent #173))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #168))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #161) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #169))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #161) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #170)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #170) #("PACKAGE" 0 7 (:parent #174))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #170) #("PATH" 0 4 (:parent #175))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #170))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #161) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #171))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #161) #(" which should have the same HASH values " 0 48 (:parent #172)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #172) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #176))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #172)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #172)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #172)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #172)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #172) #("PACKAGE" 0 7 (:parent #182))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #172) #("PATH" 0 4 (:parent #183))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #172)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #172)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #172) #("PACKAGE" 0 7 (:parent #187))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #172) #("PATH" 0 4 (:parent #188))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #172)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #172) #("PACKAGE" 0 7 (:parent #190))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #172) #("PATH" 0 4 (:parent #191))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #172)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #172)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #172)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #172) #("PACKAGE" 0 7 (:parent #197))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #172) #("PATH" 0 4 (:parent #198))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #172)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #172)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #172)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #172)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #172) #("PACKAGE" 0 7 (:parent #204))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #172) #("PATH" 0 4 (:parent #205))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #172)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #172)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow 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980)) :post-blank 0 :post-affiliated 752 :mode nil :granularity nil :parent #354) (item (:bullet "- " :begin 752 :end 834 :contents-begin 757 :contents-end 834 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 752 :tag nil :mode item :granularity nil :parent #358) (paragraph (:begin 757 :end 834 :contents-begin 757 :contents-end 834 :post-blank 0 :post-affiliated 757 :mode nil :granularity nil :parent #361) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link 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:post-affiliated 839 :mode nil :granularity nil :parent #362) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data" :application nil :search-option nil :begin 839 :end 931 :contents-begin 885 :contents-end 929 :post-blank 0 :parent #365) #("ERROR: can not find directory $HOME/gn2" 0 39 (:parent #368)) (subscript (:begin 924 :end 929 :use-brackets-p nil :contents-begin 925 :contents-end 929 :post-blank 0 :parent #368) #("data" 0 4 (:parent #372)))) #("\n" 0 1 (:parent #365)))) (item (:bullet "- " :begin 932 :end 980 :contents-begin 937 :contents-end 980 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 932 :tag nil :mode item :granularity nil :parent #358) (paragraph (:begin 937 :end 980 :contents-begin 937 :contents-end 980 :post-blank 0 :post-affiliated 937 :mode nil :granularity nil :parent #363) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 937 :end 979 :contents-begin 959 :contents-end 977 :post-blank 0 :parent #366) #("Can't run a module" 0 18 (:parent #369))) #("\n" 0 1 (:parent #366))))))))) (headline (:raw-value "Introduction" :begin 981 :end 1722 :pre-blank 1 :contents-begin 997 :contents-end 1721 :robust-begin 999 :robust-end 1719 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #343) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #346) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #353))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #350) #("GNU Guix main" 0 13 (:parent #356))) #(".\n" 0 2 (:parent #350))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #344))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #347))) :mode section :granularity nil :parent #344) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #347) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #350) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #353)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #353) #("here" 0 4 (:parent #357))) #(".\n" 0 2 (:parent #353))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #350) #("If it works you should be able to install a package with\n" 0 57 (:parent #354))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #350)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #348))) :mode nil :granularity nil :parent #344) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #348) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #351) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #354))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #351) #("#+begin" 0 7 (:parent #355)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #355) #("src" 0 3 (:parent #359))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #355)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #355)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #355)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #355)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #355) #("src" 0 3 (:parent #365))) #("bash\n" 0 5 (:parent #355))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #349))) :mode nil :granularity nil :parent #344) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #349) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #352) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #355)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #355) #("these" 0 5 (:parent #359))) #("steps carefully.\n" 0 17 (:parent #355))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #350))) :mode nil :granularity nil :parent #344) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #350) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #353) #("#+begin" 0 7 (:parent #356)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #356) #("src" 0 3 (:parent #360))) #("bash\nenv GUIX" 0 13 (:parent #356)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #356) #("PACKAGE" 0 7 (:parent #362))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #356) #("PATH" 0 4 (:parent #363))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #356)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #356) #("src" 0 3 (:parent #365))) #("bash\n" 0 5 (:parent #356))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #353) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #357)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #357)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #357))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #353) #("#+begin" 0 7 (:parent #358)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #358) #("src" 0 3 (:parent #362))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #358))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #353) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #359))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #353) #(" yes\n env GUIX" 0 30 (:parent #360)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #360) #("PACKAGE" 0 7 (:parent #364))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #360) #("PATH" 0 4 (:parent #365))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #360))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #353) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #361))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #353) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #362)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #362) #("PACKAGE" 0 7 (:parent #366))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #362) #("PATH" 0 4 (:parent #367))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #362))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #353) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #363))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #353) #(" which should have the same HASH values " 0 48 (:parent #364)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #364) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #368))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #364)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #374))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #375))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #364)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #364)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #379))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #380))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #364)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #382))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #383))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #364)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #389))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #390))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #364)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #364)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #396))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #397))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #364))))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((paragraph (:begin 125 :end 157 :contents-begin 125 :contents-end 157 :post-blank 0 :post-affiliated 125 :mode nil :granularity nil :parent (item (:bullet "- " :begin 122 :end 157 :contents-begin 125 :contents-end 157 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 122 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 122 :end 980 :contents-begin 122 :contents-end 980 :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :post-blank 0 :post-affiliated 122 :mode planning :granularity nil :parent (section (:begin 122 :end 981 :contents-begin 122 :contents-end 980 :robust-begin 122 :robust-end 978 :post-blank 1 :post-affiliated 122 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 44 :end 981 :pre-blank 0 :contents-begin 122 :contents-end 980 :robust-begin 124 :robust-end 978 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 44 :title (#("Table of Contents" 0 17 (:parent #100))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 2 :contents-end 17451 :end 17451 :robust-begin 4 :robust-end 17449 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 2 :end 44 :contents-begin 2 :contents-end 43 :robust-begin 2 :robust-end 41 :post-blank 1 :post-affiliated 2 :mode first-section :granularity nil :parent #146) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 2 :end 43 :post-blank 0 :post-affiliated 2 :mode top-comment :granularity nil :parent #149))) #100 (headline (:raw-value "Introduction" :begin 981 :end 1722 :pre-blank 1 :contents-begin 997 :contents-end 1721 :robust-begin 999 :robust-end 1719 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #151))) :mode nil :granularity nil :parent #146) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #151) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #154) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #157)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #157) #("Guix-notes" 0 10 (:parent #161))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #157))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #154) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #158)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #158) #("Guix bioinformatics" 0 19 (:parent #162))) #("and " 0 4 (:parent #158)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #158) #("GNU Guix main" 0 13 (:parent #164))) #(".\n" 0 2 (:parent #158))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #152))) :mode nil :granularity nil :parent #146) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #155))) :mode section :granularity nil :parent #152) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #155) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #158) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #161)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #161) #("here" 0 4 (:parent #165))) #(".\n" 0 2 (:parent #161))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #158) #("If it works you should be able to install a package with\n" 0 57 (:parent #162))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #158)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #156))) :mode nil :granularity nil :parent #152) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #156) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #159) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #162))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #159) #("#+begin" 0 7 (:parent #163)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #163) #("src" 0 3 (:parent #167))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #163)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #163)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #163)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #163)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #163)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #163) #("src" 0 3 (:parent #173))) #("bash\n" 0 5 (:parent #163))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #157))) :mode nil :granularity nil :parent #152) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #157) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #160) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #163)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #163) #("these" 0 5 (:parent #167))) #("steps carefully.\n" 0 17 (:parent #163))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #158))) :mode nil :granularity nil :parent #152) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #158) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #161) #("#+begin" 0 7 (:parent #164)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #164) #("src" 0 3 (:parent #168))) #("bash\nenv GUIX" 0 13 (:parent #164)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #164) #("PACKAGE" 0 7 (:parent #170))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #164) #("PATH" 0 4 (:parent #171))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #164)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #164) #("src" 0 3 (:parent #173))) #("bash\n" 0 5 (:parent #164))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #161) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #165)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #165)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #165))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #161) #("#+begin" 0 7 (:parent #166)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #166) #("src" 0 3 (:parent #170))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #166))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #161) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #167))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #161) #(" yes\n env GUIX" 0 30 (:parent #168)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #168) #("PACKAGE" 0 7 (:parent #172))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #168) #("PATH" 0 4 (:parent #173))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #168))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #161) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #169))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #161) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #170)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #170) #("PACKAGE" 0 7 (:parent #174))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #170) #("PATH" 0 4 (:parent #175))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #170))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #161) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #171))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #161) #(" which should have the same HASH values " 0 48 (:parent #172)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #172) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #176))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #172)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #172)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #172)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #172)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #172) #("PACKAGE" 0 7 (:parent #182))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #172) #("PATH" 0 4 (:parent #183))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #172)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #172)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #172) #("PACKAGE" 0 7 (:parent #187))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #172) #("PATH" 0 4 (:parent #188))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #172)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #172) #("PACKAGE" 0 7 (:parent #190))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #172) #("PATH" 0 4 (:parent #191))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #172)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #172)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #172)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #172) #("PACKAGE" 0 7 (:parent #197))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #172) #("PATH" 0 4 (:parent #198))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #172)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #172)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #172)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #172)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #172) #("PACKAGE" 0 7 (:parent #204))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #172) #("PATH" 0 4 (:parent #205))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #172)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #172)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #172)))))))) #76)) #52)) #20 (item (:bullet "- " :begin 157 :end 582 :contents-begin 160 :contents-end 582 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 157 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 160 :end 202 :contents-begin 160 :contents-end 202 :post-blank 0 :post-affiliated 160 :mode nil :granularity nil :parent #56) (link (:type "custom-id" :path "source-deployment" :format bracket :raw-link "#source-deployment" :application nil :search-option nil :begin 160 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nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 122 :end 980 :contents-begin 122 :contents-end 980 :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :post-blank 0 :post-affiliated 122 :mode planning :granularity nil :parent (section (:begin 122 :end 981 :contents-begin 122 :contents-end 980 :robust-begin 122 :robust-end 978 :post-blank 1 :post-affiliated 122 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 44 :end 981 :pre-blank 0 :contents-begin 122 :contents-end 980 :robust-begin 124 :robust-end 978 :level 1 :priority nil :tags 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:footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #152))) :mode nil :granularity nil :parent #147) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #152) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #155) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #158)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #158) #("Guix-notes" 0 10 (:parent #162))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #158))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #155) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #159)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #159) #("Guix bioinformatics" 0 19 (:parent #163))) #("and " 0 4 (:parent #159)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #159) #("GNU Guix main" 0 13 (:parent #165))) #(".\n" 0 2 (:parent #159))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #153))) :mode nil :granularity nil :parent #147) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #156))) :mode section :granularity nil :parent #153) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #156) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #159) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #162)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #162) #("here" 0 4 (:parent #166))) #(".\n" 0 2 (:parent #162))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #159) #("If it works you should be able to install a package with\n" 0 57 (:parent #163))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #159)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #157))) :mode nil :granularity nil :parent #153) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #157) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #160) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #163))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #160) #("#+begin" 0 7 (:parent #164)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #164) #("src" 0 3 (:parent #168))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #164)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #164)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #164)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #164)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #164)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #164) #("src" 0 3 (:parent #174))) #("bash\n" 0 5 (:parent #164))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #158))) :mode nil :granularity nil :parent #153) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #158) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #161) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #164)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #164) #("these" 0 5 (:parent #168))) #("steps carefully.\n" 0 17 (:parent #164))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #159))) :mode nil :granularity nil :parent #153) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #159) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #162) #("#+begin" 0 7 (:parent #165)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #165) #("src" 0 3 (:parent #169))) #("bash\nenv GUIX" 0 13 (:parent #165)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #165) #("PACKAGE" 0 7 (:parent #171))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #165) #("PATH" 0 4 (:parent #172))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #165)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #165) #("src" 0 3 (:parent #174))) #("bash\n" 0 5 (:parent #165))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #162) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #166)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #166)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #166))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #162) #("#+begin" 0 7 (:parent #167)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #167) #("src" 0 3 (:parent #171))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #167))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #162) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #168))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #162) #(" yes\n env GUIX" 0 30 (:parent #169)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #169) #("PACKAGE" 0 7 (:parent #173))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #169) #("PATH" 0 4 (:parent #174))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #169))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #162) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #170))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #162) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #171)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #171) #("PACKAGE" 0 7 (:parent #175))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #171) #("PATH" 0 4 (:parent #176))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #171))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #162) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #172))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #162) #(" which should have the same HASH values " 0 48 (:parent #173)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #173) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #177))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #173)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #173)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #173)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #173)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #173)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #173) #("PACKAGE" 0 7 (:parent #183))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #173) #("PATH" 0 4 (:parent #184))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #173)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #173)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #173)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #173) #("PACKAGE" 0 7 (:parent #188))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #173) #("PATH" 0 4 (:parent #189))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #173)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #173) #("PACKAGE" 0 7 (:parent #191))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #173) #("PATH" 0 4 (:parent #192))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #173)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #173)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #173)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #173)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #173)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #173) #("PACKAGE" 0 7 (:parent #198))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #173) #("PATH" 0 4 (:parent #199))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #173)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #173)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #173)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #173)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #173)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #173) #("PACKAGE" 0 7 (:parent #205))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #173) #("PATH" 0 4 (:parent #206))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #173)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #173)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #173)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #173)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #173)))))))) #77)) #53)) #21 (item (:bullet "- " :begin 157 :end 582 :contents-begin 160 :contents-end 582 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 157 :tag nil :mode item :granularity nil :parent #53) (paragraph (:begin 160 :end 202 :contents-begin 160 :contents-end 202 :post-blank 0 :post-affiliated 160 :mode nil :granularity nil :parent #57) (link (:type "custom-id" :path "source-deployment" :format bracket :raw-link "#source-deployment" :application nil :search-option nil :begin 160 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nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :post-blank 0 :post-affiliated 122 :mode planning :granularity nil :parent (section (:begin 122 :end 981 :contents-begin 122 :contents-end 980 :robust-begin 122 :robust-end 978 :post-blank 1 :post-affiliated 122 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 44 :end 981 :pre-blank 0 :contents-begin 122 :contents-end 980 :robust-begin 124 :robust-end 978 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 44 :title (#("Table of 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(section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #131) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #134) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #137)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #137) #("Guix-notes" 0 10 (:parent #141))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #137))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #134) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #138)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #138) #("Guix bioinformatics" 0 19 (:parent #142))) #("and " 0 4 (:parent #138)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #138) #("GNU Guix main" 0 13 (:parent #144))) #(".\n" 0 2 (:parent #138))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #132))) :mode nil :granularity nil :parent #126) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #135))) :mode section :granularity nil :parent #132) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #135) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #138) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #141)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #141) #("here" 0 4 (:parent #145))) #(".\n" 0 2 (:parent #141))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #138) #("If it works you should be able to install a package with\n" 0 57 (:parent #142))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #138)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #136))) :mode nil :granularity nil :parent #132) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #136) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #139) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #142))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #139) #("#+begin" 0 7 (:parent #143)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #143) #("src" 0 3 (:parent #147))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #143)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #143)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #143)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #143)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #143)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #143) #("src" 0 3 (:parent #153))) #("bash\n" 0 5 (:parent #143))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #137))) :mode nil :granularity nil :parent #132) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #137) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #140) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #143)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #143) #("these" 0 5 (:parent #147))) #("steps carefully.\n" 0 17 (:parent #143))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #138))) :mode nil :granularity nil :parent #132) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #138) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #141) #("#+begin" 0 7 (:parent #144)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #144) #("src" 0 3 (:parent #148))) #("bash\nenv GUIX" 0 13 (:parent #144)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #144) #("PACKAGE" 0 7 (:parent #150))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #144) #("PATH" 0 4 (:parent #151))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #144)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #144) #("src" 0 3 (:parent #153))) #("bash\n" 0 5 (:parent #144))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #141) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #145)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #145)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #145))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #141) #("#+begin" 0 7 (:parent #146)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #146) #("src" 0 3 (:parent #150))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #146))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #141) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #147))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #141) #(" yes\n env GUIX" 0 30 (:parent #148)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #148) #("PACKAGE" 0 7 (:parent #152))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #148) #("PATH" 0 4 (:parent #153))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #148))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #141) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #149))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #141) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #150)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #150) #("PACKAGE" 0 7 (:parent #154))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #150) #("PATH" 0 4 (:parent #155))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #150))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #141) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #151))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #141) #(" which should have the same HASH values " 0 48 (:parent #152)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #152) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #156))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #152)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #152)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #152)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #152)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #162))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #163))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #152)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #152)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #167))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #168))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #152)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #170))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #171))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #152)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #152)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #152)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #177))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #178))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #152)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #152)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #152)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #152)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #184))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #185))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #152)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #152)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #152)))))))) #56)) #32)) #0 (item (:bullet "- " :begin 157 :end 582 :contents-begin 160 :contents-end 582 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 157 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 160 :end 202 :contents-begin 160 :contents-end 202 :post-blank 0 :post-affiliated 160 :mode nil :granularity nil :parent #36) (link (:type "custom-id" :path "source-deployment" :format bracket :raw-link "#source-deployment" :application nil :search-option nil :begin 160 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(:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #343) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #346) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #353))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #350) #("GNU Guix main" 0 13 (:parent #356))) #(".\n" 0 2 (:parent #350))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #344))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #347))) :mode section :granularity nil :parent #344) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #347) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #350) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #353)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #353) #("here" 0 4 (:parent #357))) #(".\n" 0 2 (:parent #353))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #350) #("If it works you should be able to install a package with\n" 0 57 (:parent #354))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #350)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #348))) :mode nil :granularity nil :parent #344) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #348) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #351) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #354))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #351) #("#+begin" 0 7 (:parent #355)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #355) #("src" 0 3 (:parent #359))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #355)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #355)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #355)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #355)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #355) #("src" 0 3 (:parent #365))) #("bash\n" 0 5 (:parent #355))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #349))) :mode nil :granularity nil :parent #344) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #349) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #352) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #355)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #355) #("these" 0 5 (:parent #359))) #("steps carefully.\n" 0 17 (:parent #355))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #350))) :mode nil :granularity nil :parent #344) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #350) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #353) #("#+begin" 0 7 (:parent #356)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #356) #("src" 0 3 (:parent #360))) #("bash\nenv GUIX" 0 13 (:parent #356)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #356) #("PACKAGE" 0 7 (:parent #362))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #356) #("PATH" 0 4 (:parent #363))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #356)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #356) #("src" 0 3 (:parent #365))) #("bash\n" 0 5 (:parent #356))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #353) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #357)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #357)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #357))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #353) #("#+begin" 0 7 (:parent #358)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #358) #("src" 0 3 (:parent #362))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #358))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #353) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #359))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #353) #(" yes\n env GUIX" 0 30 (:parent #360)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #360) #("PACKAGE" 0 7 (:parent #364))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #360) #("PATH" 0 4 (:parent #365))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #360))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #353) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #361))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #353) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #362)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #362) #("PACKAGE" 0 7 (:parent #366))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #362) #("PATH" 0 4 (:parent #367))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #362))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #353) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #363))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #353) #(" which should have the same HASH values " 0 48 (:parent #364)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #364) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #368))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #364)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #374))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #375))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #364)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #364)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #379))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #380))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #364)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #382))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #383))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #364)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #389))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #390))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #364)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #364)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #396))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #397))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #364))))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((item (:bullet "- " :begin 122 :end 157 :contents-begin 125 :contents-end 157 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 122 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 122 :end 980 :contents-begin 122 :contents-end 980 :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :post-blank 0 :post-affiliated 122 :mode planning :granularity nil :parent (section (:begin 122 :end 981 :contents-begin 122 :contents-end 980 :robust-begin 122 :robust-end 978 :post-blank 1 :post-affiliated 122 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 44 :end 981 :pre-blank 0 :contents-begin 122 :contents-end 980 :robust-begin 124 :robust-end 978 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 44 :title (#("Table of Contents" 0 17 (:parent #80))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 2 :contents-end 17451 :end 17451 :robust-begin 4 :robust-end 17449 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 2 :end 44 :contents-begin 2 :contents-end 43 :robust-begin 2 :robust-end 41 :post-blank 1 :post-affiliated 2 :mode first-section :granularity nil :parent #126) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 2 :end 43 :post-blank 0 :post-affiliated 2 :mode top-comment :granularity nil :parent #129))) #80 (headline (:raw-value "Introduction" :begin 981 :end 1722 :pre-blank 1 :contents-begin 997 :contents-end 1721 :robust-begin 999 :robust-end 1719 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #131))) :mode nil :granularity nil :parent #126) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #131) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #134) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #137)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #137) #("Guix-notes" 0 10 (:parent #141))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #137))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #134) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #138)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #138) #("Guix bioinformatics" 0 19 (:parent #142))) #("and " 0 4 (:parent #138)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #138) #("GNU Guix main" 0 13 (:parent #144))) #(".\n" 0 2 (:parent #138))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #132))) :mode nil :granularity nil :parent #126) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #135))) :mode section :granularity nil :parent #132) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #135) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #138) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #141)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #141) #("here" 0 4 (:parent #145))) #(".\n" 0 2 (:parent #141))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #138) #("If it works you should be able to install a package with\n" 0 57 (:parent #142))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #138)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #136))) :mode nil :granularity nil :parent #132) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #136) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #139) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #142))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #139) #("#+begin" 0 7 (:parent #143)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #143) #("src" 0 3 (:parent #147))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #143)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #143)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #143)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #143)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #143)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #143) #("src" 0 3 (:parent #153))) #("bash\n" 0 5 (:parent #143))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #137))) :mode nil :granularity nil :parent #132) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #137) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #140) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #143)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #143) #("these" 0 5 (:parent #147))) #("steps carefully.\n" 0 17 (:parent #143))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #138))) :mode nil :granularity nil :parent #132) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #138) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #141) #("#+begin" 0 7 (:parent #144)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #144) #("src" 0 3 (:parent #148))) #("bash\nenv GUIX" 0 13 (:parent #144)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #144) #("PACKAGE" 0 7 (:parent #150))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #144) #("PATH" 0 4 (:parent #151))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #144)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #144) #("src" 0 3 (:parent #153))) #("bash\n" 0 5 (:parent #144))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #141) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #145)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #145)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #145))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #141) #("#+begin" 0 7 (:parent #146)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #146) #("src" 0 3 (:parent #150))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #146))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #141) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #147))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #141) #(" yes\n env GUIX" 0 30 (:parent #148)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #148) #("PACKAGE" 0 7 (:parent #152))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #148) #("PATH" 0 4 (:parent #153))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #148))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #141) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #149))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #141) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #150)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #150) #("PACKAGE" 0 7 (:parent #154))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #150) #("PATH" 0 4 (:parent #155))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #150))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #141) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #151))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #141) #(" which should have the same HASH values " 0 48 (:parent #152)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #152) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #156))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #152)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #152)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #152)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #152)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #162))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #163))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #152)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #152)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #167))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #168))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #152)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #170))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #171))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #152)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #152)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #152)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #177))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #178))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #152)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #152)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #152)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #152)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #184))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #185))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #152)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #152)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #152)))))))) #56)) #32)) #0 (item (:bullet "- " :begin 157 :end 582 :contents-begin 160 :contents-end 582 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 157 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 160 :end 202 :contents-begin 160 :contents-end 202 :post-blank 0 :post-affiliated 160 :mode nil :granularity nil :parent #36) (link (:type "custom-id" :path "source-deployment" :format bracket :raw-link "#source-deployment" :application nil :search-option nil :begin 160 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157 :post-blank 0 :post-affiliated 125 :mode nil :granularity nil :parent #0) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 125 :end 156 :contents-begin 142 :contents-end 154 :post-blank 0 :parent #3) #("Introduction" 0 12 (:parent #6))) #("\n" 0 1 (:parent #3))))) mapconcat(#f(compiled-function (element) #) ((item (:bullet "- " :begin 122 :end 157 :contents-begin 125 :contents-end 157 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 122 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 122 :end 980 :contents-begin 122 :contents-end 980 :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :post-blank 0 :post-affiliated 122 :mode planning :granularity nil :parent (section (:begin 122 :end 981 :contents-begin 122 :contents-end 980 :robust-begin 122 :robust-end 978 :post-blank 1 :post-affiliated 122 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 44 :end 981 :pre-blank 0 :contents-begin 122 :contents-end 980 :robust-begin 124 :robust-end 978 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 44 :title (#("Table of Contents" 0 17 (:parent #81))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 2 :contents-end 17451 :end 17451 :robust-begin 4 :robust-end 17449 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 2 :end 44 :contents-begin 2 :contents-end 43 :robust-begin 2 :robust-end 41 :post-blank 1 :post-affiliated 2 :mode first-section :granularity nil :parent #127) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 2 :end 43 :post-blank 0 :post-affiliated 2 :mode top-comment :granularity nil :parent #130))) #81 (headline (:raw-value "Introduction" :begin 981 :end 1722 :pre-blank 1 :contents-begin 997 :contents-end 1721 :robust-begin 999 :robust-end 1719 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #132))) :mode nil :granularity nil :parent #127) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #132) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #135) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #138)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #138) #("Guix-notes" 0 10 (:parent #142))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #138))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #135) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #139)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #139) #("Guix bioinformatics" 0 19 (:parent #143))) #("and " 0 4 (:parent #139)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #139) #("GNU Guix main" 0 13 (:parent #145))) #(".\n" 0 2 (:parent #139))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #133))) :mode nil :granularity nil :parent #127) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #136))) :mode section :granularity nil :parent #133) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #136) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #139) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #142)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #142) #("here" 0 4 (:parent #146))) #(".\n" 0 2 (:parent #142))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #139) #("If it works you should be able to install a package with\n" 0 57 (:parent #143))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #139)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #137))) :mode nil :granularity nil :parent #133) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #137) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #140) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #143))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #140) #("#+begin" 0 7 (:parent #144)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #144) #("src" 0 3 (:parent #148))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #144)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #144)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #144)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #144)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #144)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #144) #("src" 0 3 (:parent #154))) #("bash\n" 0 5 (:parent #144))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #138))) :mode nil :granularity nil :parent #133) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #138) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #141) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #144)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #144) #("these" 0 5 (:parent #148))) #("steps carefully.\n" 0 17 (:parent #144))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #139))) :mode nil :granularity nil :parent #133) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #139) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #142) #("#+begin" 0 7 (:parent #145)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #145) #("src" 0 3 (:parent #149))) #("bash\nenv GUIX" 0 13 (:parent #145)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #145) #("PACKAGE" 0 7 (:parent #151))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #145) #("PATH" 0 4 (:parent #152))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #145)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #145) #("src" 0 3 (:parent #154))) #("bash\n" 0 5 (:parent #145))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #142) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #146)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #146)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #146))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #142) #("#+begin" 0 7 (:parent #147)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #147) #("src" 0 3 (:parent #151))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #147))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #142) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #148))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #142) #(" yes\n env GUIX" 0 30 (:parent #149)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #149) #("PACKAGE" 0 7 (:parent #153))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #149) #("PATH" 0 4 (:parent #154))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #149))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #142) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #150))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #142) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #151)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #151) #("PACKAGE" 0 7 (:parent #155))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #151) #("PATH" 0 4 (:parent #156))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #151))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #142) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #152))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #142) #(" which should have the same HASH values " 0 48 (:parent #153)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #153) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #157))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #153)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #153)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #153)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #153)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #153) #("PACKAGE" 0 7 (:parent #163))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #153) #("PATH" 0 4 (:parent #164))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #153)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #153)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #153) #("PACKAGE" 0 7 (:parent #168))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #153) #("PATH" 0 4 (:parent #169))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #153)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #153) #("PACKAGE" 0 7 (:parent #171))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #153) #("PATH" 0 4 (:parent #172))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #153)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #153)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #153)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #153) #("PACKAGE" 0 7 (:parent #178))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #153) #("PATH" 0 4 (:parent #179))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #153)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #153)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #153)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #153)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #153) #("PACKAGE" 0 7 (:parent #185))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #153) #("PATH" 0 4 (:parent #186))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #153)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #153)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #153)))))))) #57)) #33)) . #0)) (paragraph (:begin 125 :end 157 :contents-begin 125 :contents-end 157 :post-blank 0 :post-affiliated 125 :mode nil :granularity nil :parent #1) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 125 :end 156 :contents-begin 142 :contents-end 154 :post-blank 0 :parent #4) #("Introduction" 0 12 (:parent #7))) #("\n" 0 1 (:parent #4)))) (item (:bullet "- " :begin 157 :end 582 :contents-begin 160 :contents-end 582 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 157 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 122 :end 980 :contents-begin 122 :contents-end 980 :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :post-blank 0 :post-affiliated 122 :mode planning :granularity nil :parent (section (:begin 122 :end 981 :contents-begin 122 :contents-end 980 :robust-begin 122 :robust-end 978 :post-blank 1 :post-affiliated 122 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 44 :end 981 :pre-blank 0 :contents-begin 122 :contents-end 980 :robust-begin 124 :robust-end 978 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 44 :title (#("Table of Contents" 0 17 (:parent #82))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 2 :contents-end 17451 :end 17451 :robust-begin 4 :robust-end 17449 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 2 :end 44 :contents-begin 2 :contents-end 43 :robust-begin 2 :robust-end 41 :post-blank 1 :post-affiliated 2 :mode first-section :granularity nil :parent #128) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 2 :end 43 :post-blank 0 :post-affiliated 2 :mode top-comment :granularity nil :parent #131))) #82 (headline (:raw-value "Introduction" :begin 981 :end 1722 :pre-blank 1 :contents-begin 997 :contents-end 1721 :robust-begin 999 :robust-end 1719 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #133))) :mode nil :granularity nil :parent #128) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #133) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #136) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #139)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #139) #("Guix-notes" 0 10 (:parent #143))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #139))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #136) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #140)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #140) #("Guix bioinformatics" 0 19 (:parent #144))) #("and " 0 4 (:parent #140)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #140) #("GNU Guix main" 0 13 (:parent #146))) #(".\n" 0 2 (:parent #140))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #134))) :mode nil :granularity nil :parent #128) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #137))) :mode section :granularity nil :parent #134) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #137) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #140) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #143)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #143) #("here" 0 4 (:parent #147))) #(".\n" 0 2 (:parent #143))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #140) #("If it works you should be able to install a package with\n" 0 57 (:parent #144))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #140)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #138))) :mode nil :granularity nil :parent #134) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #138) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #141) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #144))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #141) #("#+begin" 0 7 (:parent #145)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #145) #("src" 0 3 (:parent #149))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #145)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #145)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #145)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #145)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #145)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #145) #("src" 0 3 (:parent #155))) #("bash\n" 0 5 (:parent #145))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #139))) :mode nil :granularity nil :parent #134) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #139) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #142) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #145)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #145) #("these" 0 5 (:parent #149))) #("steps carefully.\n" 0 17 (:parent #145))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #140))) :mode nil :granularity nil :parent #134) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #140) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #143) #("#+begin" 0 7 (:parent #146)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #146) #("src" 0 3 (:parent #150))) #("bash\nenv GUIX" 0 13 (:parent #146)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #146) #("PACKAGE" 0 7 (:parent #152))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #146) #("PATH" 0 4 (:parent #153))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #146)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #146) #("src" 0 3 (:parent #155))) #("bash\n" 0 5 (:parent #146))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #143) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #147)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #147)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #147))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #143) #("#+begin" 0 7 (:parent #148)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #148) #("src" 0 3 (:parent #152))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #148))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #143) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #149))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #143) #(" yes\n env GUIX" 0 30 (:parent #150)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #150) #("PACKAGE" 0 7 (:parent #154))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #150) #("PATH" 0 4 (:parent #155))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #150))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #143) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #151))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #143) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #152)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #156))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #157))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #152))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #143) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #153))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #143) #(" which should have the same HASH values " 0 48 (:parent #154)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #154) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #158))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #154)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #154)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #154)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #154)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #154) #("PACKAGE" 0 7 (:parent #164))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #154) #("PATH" 0 4 (:parent #165))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #154)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #154)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #154) #("PACKAGE" 0 7 (:parent #169))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #154) #("PATH" 0 4 (:parent #170))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #154)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #154) #("PACKAGE" 0 7 (:parent #172))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #154) #("PATH" 0 4 (:parent #173))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #154)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #154)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #154)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #154) #("PACKAGE" 0 7 (:parent #179))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #154) #("PATH" 0 4 (:parent #180))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #154)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #154)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #154)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #154)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #154) #("PACKAGE" 0 7 (:parent #186))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #154) #("PATH" 0 4 (:parent #187))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #154)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #154)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #154)))))))) #58)) #34)) . #0)) (paragraph (:begin 160 :end 202 :contents-begin 160 :contents-end 202 :post-blank 0 :post-affiliated 160 :mode nil :granularity nil :parent #2) (link (:type "custom-id" :path "source-deployment" :format bracket :raw-link "#source-deployment" :application nil :search-option nil :begin 160 :end 201 :contents-begin 182 :contents-end 199 :post-blank 0 :parent #5) #("Source deployment" 0 17 (:parent #8))) #("\n" 0 1 (:parent #5))) (plain-list (:type unordered :begin 202 :end 582 :contents-begin 202 :contents-end 582 :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #140)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #140) #("Guix-notes" 0 10 (:parent #144))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #140))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #137) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #141)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #141) #("Guix bioinformatics" 0 19 (:parent #145))) #("and " 0 4 (:parent #141)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #141) #("GNU Guix main" 0 13 (:parent #147))) #(".\n" 0 2 (:parent #141))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #135))) :mode nil :granularity nil :parent #129) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #138))) :mode section :granularity nil :parent #135) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #138) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #141) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #144)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #144) #("here" 0 4 (:parent #148))) #(".\n" 0 2 (:parent #144))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #141) #("If it works you should be able to install a package with\n" 0 57 (:parent #145))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #141)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #139))) :mode nil :granularity nil :parent #135) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #139) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #142) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #145))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #142) #("#+begin" 0 7 (:parent #146)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #146) #("src" 0 3 (:parent #150))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #146)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #146)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #146)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #146)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #146)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #146) #("src" 0 3 (:parent #156))) #("bash\n" 0 5 (:parent #146))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #140))) :mode nil :granularity nil :parent #135) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #140) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #143) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #146)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #146) #("these" 0 5 (:parent #150))) #("steps carefully.\n" 0 17 (:parent #146))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #141))) :mode nil :granularity nil :parent #135) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #141) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #144) #("#+begin" 0 7 (:parent #147)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #147) #("src" 0 3 (:parent #151))) #("bash\nenv GUIX" 0 13 (:parent #147)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #147) #("PACKAGE" 0 7 (:parent #153))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #147) #("PATH" 0 4 (:parent #154))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #147)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #147) #("src" 0 3 (:parent #156))) #("bash\n" 0 5 (:parent #147))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #144) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #148)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #148)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #148))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #144) #("#+begin" 0 7 (:parent #149)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #149) #("src" 0 3 (:parent #153))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #149))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #144) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #150))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #144) #(" yes\n env GUIX" 0 30 (:parent #151)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #151) #("PACKAGE" 0 7 (:parent #155))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #151) #("PATH" 0 4 (:parent #156))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #151))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #144) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #152))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #144) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #153)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #153) #("PACKAGE" 0 7 (:parent #157))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #153) #("PATH" 0 4 (:parent #158))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #153))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #144) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #154))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #144) #(" which should have the same HASH values " 0 48 (:parent #155)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #155) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #159))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #155)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #155)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #155)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #155)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #155) #("PACKAGE" 0 7 (:parent #165))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #155) #("PATH" 0 4 (:parent #166))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #155)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #155)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #155) #("PACKAGE" 0 7 (:parent #170))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #155) #("PATH" 0 4 (:parent #171))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #155)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #155) #("PACKAGE" 0 7 (:parent #173))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #155) #("PATH" 0 4 (:parent #174))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #155)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #155)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #155)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #155) #("PACKAGE" 0 7 (:parent #180))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #155) #("PATH" 0 4 (:parent #181))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #155)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #155)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #155)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #155)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #155) #("PACKAGE" 0 7 (:parent #187))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #155) #("PATH" 0 4 (:parent #188))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #155)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #155)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #155)))))))) #59)) #35)) . #0)) (paragraph (:begin 585 :end 709 :contents-begin 585 :contents-end 709 :post-blank 0 :post-affiliated 585 :mode nil :granularity nil :parent #3) (link (:type "custom-id" :path "source-deployment-and-other-information-on-reproducibility" :format bracket :raw-link "#source-deployment-and-other-information-on-reproducibility" :application nil :search-option nil :begin 585 :end 708 :contents-begin 648 :contents-end 706 :post-blank 0 :parent #6) #("Source deployment and other information on reproducibility" 0 58 (:parent #9))) #("\n" 0 1 (:parent #6)))) (item (:bullet "- " :begin 709 :end 980 :contents-begin 712 :contents-end 980 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 709 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 122 :end 980 :contents-begin 122 :contents-end 980 :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :post-blank 0 :post-affiliated 122 :mode planning :granularity nil :parent (section (:begin 122 :end 981 :contents-begin 122 :contents-end 980 :robust-begin 122 :robust-end 978 :post-blank 1 :post-affiliated 122 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 44 :end 981 :pre-blank 0 :contents-begin 122 :contents-end 980 :robust-begin 124 :robust-end 978 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 44 :title (#("Table of Contents" 0 17 (:parent #84))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 2 :contents-end 17451 :end 17451 :robust-begin 4 :robust-end 17449 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 2 :end 44 :contents-begin 2 :contents-end 43 :robust-begin 2 :robust-end 41 :post-blank 1 :post-affiliated 2 :mode first-section :granularity nil :parent #130) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 2 :end 43 :post-blank 0 :post-affiliated 2 :mode top-comment :granularity nil :parent #133))) #84 (headline (:raw-value "Introduction" :begin 981 :end 1722 :pre-blank 1 :contents-begin 997 :contents-end 1721 :robust-begin 999 :robust-end 1719 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #135))) :mode nil :granularity nil :parent #130) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #135) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #138) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #141)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #141) #("Guix-notes" 0 10 (:parent #145))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #141))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #138) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #142)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #142) #("Guix bioinformatics" 0 19 (:parent #146))) #("and " 0 4 (:parent #142)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #142) #("GNU Guix main" 0 13 (:parent #148))) #(".\n" 0 2 (:parent #142))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #136))) :mode nil :granularity nil :parent #130) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #139))) :mode section :granularity nil :parent #136) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #139) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #142) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #145)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #145) #("here" 0 4 (:parent #149))) #(".\n" 0 2 (:parent #145))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #142) #("If it works you should be able to install a package with\n" 0 57 (:parent #146))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #142)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #140))) :mode nil :granularity nil :parent #136) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #140) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #143) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #146))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #143) #("#+begin" 0 7 (:parent #147)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #147) #("src" 0 3 (:parent #151))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #147)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #147)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #147)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #147)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #147)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #147) #("src" 0 3 (:parent #157))) #("bash\n" 0 5 (:parent #147))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #141))) :mode nil :granularity nil :parent #136) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #141) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #144) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #147)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #147) #("these" 0 5 (:parent #151))) #("steps carefully.\n" 0 17 (:parent #147))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #142))) :mode nil :granularity nil :parent #136) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #142) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #145) #("#+begin" 0 7 (:parent #148)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #148) #("src" 0 3 (:parent #152))) #("bash\nenv GUIX" 0 13 (:parent #148)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #148) #("PACKAGE" 0 7 (:parent #154))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #148) #("PATH" 0 4 (:parent #155))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #148)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #148) #("src" 0 3 (:parent #157))) #("bash\n" 0 5 (:parent #148))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #145) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #149)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #149)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #149))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #145) #("#+begin" 0 7 (:parent #150)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #150) #("src" 0 3 (:parent #154))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #150))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #145) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #151))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #145) #(" yes\n env GUIX" 0 30 (:parent #152)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #156))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #157))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #152))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #145) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #153))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #145) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #154)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #154) #("PACKAGE" 0 7 (:parent #158))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #154) #("PATH" 0 4 (:parent #159))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #154))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #145) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #155))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #145) #(" which should have the same HASH values " 0 48 (:parent #156)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #156) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #160))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #156)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #156)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #156)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #156)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #156) #("PACKAGE" 0 7 (:parent #166))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #156) #("PATH" 0 4 (:parent #167))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #156)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #156)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #156) #("PACKAGE" 0 7 (:parent #171))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #156) #("PATH" 0 4 (:parent #172))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #156)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #156) #("PACKAGE" 0 7 (:parent #174))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #156) #("PATH" 0 4 (:parent #175))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #156)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #156)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #156)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #156) #("PACKAGE" 0 7 (:parent #181))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #156) #("PATH" 0 4 (:parent #182))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #156)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #156)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #156)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #156)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #156) #("PACKAGE" 0 7 (:parent #188))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #156) #("PATH" 0 4 (:parent #189))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #156)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #156)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #156)))))))) #60)) #36)) . #0)) (paragraph (:begin 712 :end 752 :contents-begin 712 :contents-end 752 :post-blank 0 :post-affiliated 712 :mode nil :granularity nil :parent #4) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 712 :end 751 :contents-begin 733 :contents-end 749 :post-blank 0 :parent #7) #("Trouble shooting" 0 16 (:parent #10))) #("\n" 0 1 (:parent #7))) (plain-list (:type unordered :begin 752 :end 980 :contents-begin 752 :contents-end 980 :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 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:contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #102) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #105)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #105) #("Guix-notes" 0 10 (:parent #109))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #105))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #102) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #106)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #106) #("Guix bioinformatics" 0 19 (:parent #110))) #("and " 0 4 (:parent #106)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #106) #("GNU Guix main" 0 13 (:parent #112))) #(".\n" 0 2 (:parent #106))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #100))) :mode nil :granularity nil :parent #94) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #103))) :mode section :granularity nil :parent #100) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #103) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #106) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #109)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #109) #("here" 0 4 (:parent #113))) #(".\n" 0 2 (:parent #109))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #106) #("If it works you should be able to install a package with\n" 0 57 (:parent #110))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #106)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #104))) :mode nil :granularity nil :parent #100) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #104) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #107) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #110))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #107) #("#+begin" 0 7 (:parent #111)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #111) #("src" 0 3 (:parent #115))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #111)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #111)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #111)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #111)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #111)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #111) #("src" 0 3 (:parent #121))) #("bash\n" 0 5 (:parent #111))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #105))) :mode nil :granularity nil :parent #100) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #105) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #108) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #111)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #111) #("these" 0 5 (:parent #115))) #("steps carefully.\n" 0 17 (:parent #111))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #106))) :mode nil :granularity nil :parent #100) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #106) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #109) #("#+begin" 0 7 (:parent #112)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #112) #("src" 0 3 (:parent #116))) #("bash\nenv GUIX" 0 13 (:parent #112)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #112) #("PACKAGE" 0 7 (:parent #118))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #112) #("PATH" 0 4 (:parent #119))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #112)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #112) #("src" 0 3 (:parent #121))) #("bash\n" 0 5 (:parent #112))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #109) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #113)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #113)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #113))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #109) #("#+begin" 0 7 (:parent #114)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #114) #("src" 0 3 (:parent #118))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #114))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #109) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #115))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #109) #(" yes\n env GUIX" 0 30 (:parent #116)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #116) #("PACKAGE" 0 7 (:parent #120))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #116) #("PATH" 0 4 (:parent #121))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #116))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #109) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #117))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #109) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #118)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #118) #("PACKAGE" 0 7 (:parent #122))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #118) #("PATH" 0 4 (:parent #123))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #118))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #109) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #119))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #109) #(" which should have the same HASH values " 0 48 (:parent #120)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #120) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #124))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #120)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #120)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #120)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #120)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #120) #("PACKAGE" 0 7 (:parent #130))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #120) #("PATH" 0 4 (:parent #131))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #120)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #120)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #120) #("PACKAGE" 0 7 (:parent #135))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #120) #("PATH" 0 4 (:parent #136))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #120)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #120) #("PACKAGE" 0 7 (:parent #138))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #120) #("PATH" 0 4 (:parent #139))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #120)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #120)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #120)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #120) #("PACKAGE" 0 7 (:parent #145))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #120) #("PATH" 0 4 (:parent #146))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #120)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #120)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #120)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #120)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #120) #("PACKAGE" 0 7 (:parent #152))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #120) #("PATH" 0 4 (:parent #153))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #120)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #120)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow 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(:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #343) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #346) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #353))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #350) #("GNU Guix main" 0 13 (:parent #356))) #(".\n" 0 2 (:parent #350))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #344))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #347))) :mode section :granularity nil :parent #344) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #347) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #350) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #353)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #353) #("here" 0 4 (:parent #357))) #(".\n" 0 2 (:parent #353))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #350) #("If it works you should be able to install a package with\n" 0 57 (:parent #354))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #350)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #348))) :mode nil :granularity nil :parent #344) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #348) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #351) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #354))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #351) #("#+begin" 0 7 (:parent #355)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #355) #("src" 0 3 (:parent #359))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #355)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #355)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #355)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #355)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #355) #("src" 0 3 (:parent #365))) #("bash\n" 0 5 (:parent #355))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #349))) :mode nil :granularity nil :parent #344) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #349) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #352) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #355)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #355) #("these" 0 5 (:parent #359))) #("steps carefully.\n" 0 17 (:parent #355))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #350))) :mode nil :granularity nil :parent #344) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #350) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #353) #("#+begin" 0 7 (:parent #356)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #356) #("src" 0 3 (:parent #360))) #("bash\nenv GUIX" 0 13 (:parent #356)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #356) #("PACKAGE" 0 7 (:parent #362))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #356) #("PATH" 0 4 (:parent #363))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #356)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #356) #("src" 0 3 (:parent #365))) #("bash\n" 0 5 (:parent #356))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #353) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #357)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #357)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #357))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #353) #("#+begin" 0 7 (:parent #358)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #358) #("src" 0 3 (:parent #362))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #358))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #353) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #359))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #353) #(" yes\n env GUIX" 0 30 (:parent #360)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #360) #("PACKAGE" 0 7 (:parent #364))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #360) #("PATH" 0 4 (:parent #365))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #360))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #353) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #361))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #353) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #362)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #362) #("PACKAGE" 0 7 (:parent #366))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #362) #("PATH" 0 4 (:parent #367))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #362))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #353) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #363))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #353) #(" which should have the same HASH values " 0 48 (:parent #364)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #364) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #368))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #364)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #374))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #375))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #364)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #364)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #379))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #380))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #364)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #382))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #383))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #364)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #389))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #390))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #364)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #364)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #396))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #397))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #364))))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((plain-list (:type unordered :begin 122 :end 980 :contents-begin 122 :contents-end 980 :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :post-blank 0 :post-affiliated 122 :mode planning :granularity nil :parent (section (:begin 122 :end 981 :contents-begin 122 :contents-end 980 :robust-begin 122 :robust-end 978 :post-blank 1 :post-affiliated 122 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 44 :end 981 :pre-blank 0 :contents-begin 122 :contents-end 980 :robust-begin 124 :robust-end 978 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 44 :title (#("Table of Contents" 0 17 (:parent #48))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 2 :contents-end 17451 :end 17451 :robust-begin 4 :robust-end 17449 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 2 :end 44 :contents-begin 2 :contents-end 43 :robust-begin 2 :robust-end 41 :post-blank 1 :post-affiliated 2 :mode first-section :granularity nil :parent #94) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 2 :end 43 :post-blank 0 :post-affiliated 2 :mode top-comment :granularity nil :parent #97))) #48 (headline (:raw-value "Introduction" :begin 981 :end 1722 :pre-blank 1 :contents-begin 997 :contents-end 1721 :robust-begin 999 :robust-end 1719 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #99))) :mode nil :granularity nil :parent #94) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #99) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #102) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #105)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #105) #("Guix-notes" 0 10 (:parent #109))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #105))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #102) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #106)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #106) #("Guix bioinformatics" 0 19 (:parent #110))) #("and " 0 4 (:parent #106)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #106) #("GNU Guix main" 0 13 (:parent #112))) #(".\n" 0 2 (:parent #106))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #100))) :mode nil :granularity nil :parent #94) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #103))) :mode section :granularity nil :parent #100) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #103) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #106) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #109)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #109) #("here" 0 4 (:parent #113))) #(".\n" 0 2 (:parent #109))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #106) #("If it works you should be able to install a package with\n" 0 57 (:parent #110))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #106)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #104))) :mode nil :granularity nil :parent #100) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #104) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #107) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #110))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #107) #("#+begin" 0 7 (:parent #111)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #111) #("src" 0 3 (:parent #115))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #111)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #111)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #111)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #111)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #111)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #111) #("src" 0 3 (:parent #121))) #("bash\n" 0 5 (:parent #111))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #105))) :mode nil :granularity nil :parent #100) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #105) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #108) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #111)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #111) #("these" 0 5 (:parent #115))) #("steps carefully.\n" 0 17 (:parent #111))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #106))) :mode nil :granularity nil :parent #100) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #106) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #109) #("#+begin" 0 7 (:parent #112)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #112) #("src" 0 3 (:parent #116))) #("bash\nenv GUIX" 0 13 (:parent #112)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #112) #("PACKAGE" 0 7 (:parent #118))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #112) #("PATH" 0 4 (:parent #119))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #112)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #112) #("src" 0 3 (:parent #121))) #("bash\n" 0 5 (:parent #112))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #109) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #113)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #113)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #113))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #109) #("#+begin" 0 7 (:parent #114)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #114) #("src" 0 3 (:parent #118))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #114))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #109) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #115))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #109) #(" yes\n env GUIX" 0 30 (:parent #116)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #116) #("PACKAGE" 0 7 (:parent #120))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #116) #("PATH" 0 4 (:parent #121))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #116))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #109) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #117))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #109) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #118)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #118) #("PACKAGE" 0 7 (:parent #122))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #118) #("PATH" 0 4 (:parent #123))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #118))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #109) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #119))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #109) #(" which should have the same HASH values " 0 48 (:parent #120)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #120) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #124))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #120)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #120)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #120)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #120)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #120) #("PACKAGE" 0 7 (:parent #130))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #120) #("PATH" 0 4 (:parent #131))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #120)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #120)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #120) #("PACKAGE" 0 7 (:parent #135))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #120) #("PATH" 0 4 (:parent #136))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #120)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #120) #("PACKAGE" 0 7 (:parent #138))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #120) #("PATH" 0 4 (:parent #139))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #120)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #120)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #120)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #120) #("PACKAGE" 0 7 (:parent #145))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #120) #("PATH" 0 4 (:parent #146))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #120)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #120)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #120)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #120)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #120) #("PACKAGE" 0 7 (:parent #152))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #120) #("PATH" 0 4 (:parent #153))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #120)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #120)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #120)))))))) #24)) #0)) (item (:bullet "- " :begin 122 :end 157 :contents-begin 125 :contents-end 157 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 122 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 125 :end 157 :contents-begin 125 :contents-end 157 :post-blank 0 :post-affiliated 125 :mode nil :granularity nil :parent #3) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 125 :end 156 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:footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #100))) :mode nil :granularity nil :parent #95) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #100) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #103) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #106)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #106) #("Guix-notes" 0 10 (:parent #110))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #106))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #103) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #107)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #107) #("Guix bioinformatics" 0 19 (:parent #111))) #("and " 0 4 (:parent #107)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #107) #("GNU Guix main" 0 13 (:parent #113))) #(".\n" 0 2 (:parent #107))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #101))) :mode nil :granularity nil :parent #95) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #104))) :mode section :granularity nil :parent #101) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #104) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #107) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #110)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #110) #("here" 0 4 (:parent #114))) #(".\n" 0 2 (:parent #110))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #107) #("If it works you should be able to install a package with\n" 0 57 (:parent #111))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #107)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #105))) :mode nil :granularity nil :parent #101) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #105) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #108) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #111))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #108) #("#+begin" 0 7 (:parent #112)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #112) #("src" 0 3 (:parent #116))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #112)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #112)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #112)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #112)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #112)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #112) #("src" 0 3 (:parent #122))) #("bash\n" 0 5 (:parent #112))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #106))) :mode nil :granularity nil :parent #101) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #106) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #109) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #112)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #112) #("these" 0 5 (:parent #116))) #("steps carefully.\n" 0 17 (:parent #112))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #107))) :mode nil :granularity nil :parent #101) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #107) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #110) #("#+begin" 0 7 (:parent #113)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #113) #("src" 0 3 (:parent #117))) #("bash\nenv GUIX" 0 13 (:parent #113)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #113) #("PACKAGE" 0 7 (:parent #119))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #113) #("PATH" 0 4 (:parent #120))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #113)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #113) #("src" 0 3 (:parent #122))) #("bash\n" 0 5 (:parent #113))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #110) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #114)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #114)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #114))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #110) #("#+begin" 0 7 (:parent #115)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #115) #("src" 0 3 (:parent #119))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #115))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #110) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #116))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #110) #(" yes\n env GUIX" 0 30 (:parent #117)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #117) #("PACKAGE" 0 7 (:parent #121))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #117) #("PATH" 0 4 (:parent #122))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #117))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #110) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #118))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #110) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #119)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #119) #("PACKAGE" 0 7 (:parent #123))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #119) #("PATH" 0 4 (:parent #124))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #119))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #110) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #120))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #110) #(" which should have the same HASH values " 0 48 (:parent #121)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #121) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #125))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #121)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #121)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #121)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #121)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #121)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #121) #("PACKAGE" 0 7 (:parent #131))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #121) #("PATH" 0 4 (:parent #132))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #121)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #121)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #121)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #121) #("PACKAGE" 0 7 (:parent #136))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #121) #("PATH" 0 4 (:parent #137))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #121)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #121) #("PACKAGE" 0 7 (:parent #139))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #121) #("PATH" 0 4 (:parent #140))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #121)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #121)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #121)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #121)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #121)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #121) #("PACKAGE" 0 7 (:parent #146))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #121) #("PATH" 0 4 (:parent #147))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #121)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #121)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #121)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #121)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #121)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #121) #("PACKAGE" 0 7 (:parent #153))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #121) #("PATH" 0 4 (:parent #154))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #121)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #121)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #121)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #121)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #121)))))))) #25)) . #0)) (item (:bullet "- " :begin 122 :end 157 :contents-begin 125 :contents-end 157 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 122 :tag nil :mode item :granularity nil :parent #1) (paragraph (:begin 125 :end 157 :contents-begin 125 :contents-end 157 :post-blank 0 :post-affiliated 125 :mode nil :granularity nil :parent #4) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 125 :end 156 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(582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 834 :tag nil :mode item :granularity nil :parent #11) (paragraph (:begin 839 :end 932 :contents-begin 839 :contents-end 932 :post-blank 0 :post-affiliated 839 :mode nil :granularity nil :parent #15) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data" :application nil :search-option nil :begin 839 :end 931 :contents-begin 885 :contents-end 929 :post-blank 0 :parent #18) #("ERROR: can not find directory $HOME/gn2" 0 39 (:parent #21)) (subscript (:begin 924 :end 929 :use-brackets-p nil :contents-begin 925 :contents-end 929 :post-blank 0 :parent #21) #("data" 0 4 (:parent #25)))) #("\n" 0 1 (:parent #18)))) (item (:bullet "- " :begin 932 :end 980 :contents-begin 937 :contents-end 980 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 932 :tag nil :mode item :granularity nil :parent #11) (paragraph (:begin 937 :end 980 :contents-begin 937 :contents-end 980 :post-blank 0 :post-affiliated 937 :mode nil :granularity nil :parent #16) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 937 :end 979 :contents-begin 959 :contents-end 977 :post-blank 0 :parent #19) #("Can't run a module" 0 18 (:parent #22))) #("\n" 0 1 (:parent #19)))))))) "") org-export-data((section (:begin 122 :end 981 :contents-begin 122 :contents-end 980 :robust-begin 122 :robust-end 978 :post-blank 1 :post-affiliated 122 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 44 :end 981 :pre-blank 0 :contents-begin 122 :contents-end 980 :robust-begin 124 :robust-end 978 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 44 :title (#("Table of Contents" 0 17 (:parent #24))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 2 :contents-end 17451 :end 17451 :robust-begin 4 :robust-end 17449 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 2 :end 44 :contents-begin 2 :contents-end 43 :robust-begin 2 :robust-end 41 :post-blank 1 :post-affiliated 2 :mode first-section :granularity nil :parent #70) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 2 :end 43 :post-blank 0 :post-affiliated 2 :mode top-comment :granularity nil :parent #73))) #24 (headline (:raw-value "Introduction" :begin 981 :end 1722 :pre-blank 1 :contents-begin 997 :contents-end 1721 :robust-begin 999 :robust-end 1719 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #75))) :mode nil :granularity nil :parent #70) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #75) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #78) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #81)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #81) #("Guix-notes" 0 10 (:parent #85))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #81))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #78) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #82)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #82) #("Guix bioinformatics" 0 19 (:parent #86))) #("and " 0 4 (:parent #82)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #82) #("GNU Guix main" 0 13 (:parent #88))) #(".\n" 0 2 (:parent #82))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #76))) :mode nil :granularity nil :parent #70) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #79))) :mode section :granularity nil :parent #76) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #79) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #82) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #85)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #85) #("here" 0 4 (:parent #89))) #(".\n" 0 2 (:parent #85))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #82) #("If it works you should be able to install a package with\n" 0 57 (:parent #86))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #82)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #80))) :mode nil :granularity nil :parent #76) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #80) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #83) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #86))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #83) #("#+begin" 0 7 (:parent #87)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #87) #("src" 0 3 (:parent #91))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #87)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #87)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #87)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #87)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #87)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #87) #("src" 0 3 (:parent #97))) #("bash\n" 0 5 (:parent #87))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #81))) :mode nil :granularity nil :parent #76) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #81) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #84) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #87)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #87) #("these" 0 5 (:parent #91))) #("steps carefully.\n" 0 17 (:parent #87))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #82))) :mode nil :granularity nil :parent #76) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #82) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #85) #("#+begin" 0 7 (:parent #88)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #88) #("src" 0 3 (:parent #92))) #("bash\nenv GUIX" 0 13 (:parent #88)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #88) #("PACKAGE" 0 7 (:parent #94))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #88) #("PATH" 0 4 (:parent #95))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #88)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #88) #("src" 0 3 (:parent #97))) #("bash\n" 0 5 (:parent #88))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #85) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #89)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #89)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #89))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #85) #("#+begin" 0 7 (:parent #90)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #90) #("src" 0 3 (:parent #94))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #90))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #85) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #91))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #85) #(" yes\n env GUIX" 0 30 (:parent #92)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #92) #("PACKAGE" 0 7 (:parent #96))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #92) #("PATH" 0 4 (:parent #97))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #92))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #85) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #93))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #85) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #94)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #94) #("PACKAGE" 0 7 (:parent #98))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #94) #("PATH" 0 4 (:parent #99))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #94))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #85) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #95))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #85) #(" which should have the same HASH values " 0 48 (:parent #96)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #96) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #100))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #96)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #96)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #96)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #96)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #96) #("PACKAGE" 0 7 (:parent #106))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #96) #("PATH" 0 4 (:parent #107))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #96)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #96)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #96) #("PACKAGE" 0 7 (:parent #111))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #96) #("PATH" 0 4 (:parent #112))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #96)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #96) #("PACKAGE" 0 7 (:parent #114))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #96) #("PATH" 0 4 (:parent #115))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #96)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #96)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #96)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #96) #("PACKAGE" 0 7 (:parent #121))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #96) #("PATH" 0 4 (:parent #122))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #96)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #96)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #96)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #96)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #96) #("PACKAGE" 0 7 (:parent #128))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #96) #("PATH" 0 4 (:parent #129))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #96)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #96)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #96)))))))) #0)) (plain-list (:type unordered :begin 122 :end 980 :contents-begin 122 :contents-end 980 :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :post-blank 0 :post-affiliated 122 :mode planning :granularity nil :parent #0) (item (:bullet "- " :begin 122 :end 157 :contents-begin 125 :contents-end 157 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #353))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #350) #("GNU Guix main" 0 13 (:parent #356))) #(".\n" 0 2 (:parent #350))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #344))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #347))) :mode section :granularity nil :parent #344) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #347) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #350) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #353)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #353) #("here" 0 4 (:parent #357))) #(".\n" 0 2 (:parent #353))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #350) #("If it works you should be able to install a package with\n" 0 57 (:parent #354))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #350)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #348))) :mode nil :granularity nil :parent #344) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #348) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #351) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #354))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #351) #("#+begin" 0 7 (:parent #355)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #355) #("src" 0 3 (:parent #359))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #355)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #355)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #355)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #355)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #355) #("src" 0 3 (:parent #365))) #("bash\n" 0 5 (:parent #355))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #349))) :mode nil :granularity nil :parent #344) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #349) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #352) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #355)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #355) #("these" 0 5 (:parent #359))) #("steps carefully.\n" 0 17 (:parent #355))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #350))) :mode nil :granularity nil :parent #344) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #350) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #353) #("#+begin" 0 7 (:parent #356)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #356) #("src" 0 3 (:parent #360))) #("bash\nenv GUIX" 0 13 (:parent #356)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #356) #("PACKAGE" 0 7 (:parent #362))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #356) #("PATH" 0 4 (:parent #363))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #356)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #356) #("src" 0 3 (:parent #365))) #("bash\n" 0 5 (:parent #356))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #353) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #357)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #357)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #357))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #353) #("#+begin" 0 7 (:parent #358)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #358) #("src" 0 3 (:parent #362))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #358))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #353) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #359))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #353) #(" yes\n env GUIX" 0 30 (:parent #360)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #360) #("PACKAGE" 0 7 (:parent #364))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #360) #("PATH" 0 4 (:parent #365))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #360))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #353) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #361))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #353) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #362)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #362) #("PACKAGE" 0 7 (:parent #366))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #362) #("PATH" 0 4 (:parent #367))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #362))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #353) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #363))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #353) #(" which should have the same HASH values " 0 48 (:parent #364)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #364) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #368))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #364)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #374))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #375))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #364)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #364)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #379))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #380))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #364)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #382))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #383))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #364)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #389))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #390))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #364)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #364)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #396))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #397))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #364))))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((section (:begin 122 :end 981 :contents-begin 122 :contents-end 980 :robust-begin 122 :robust-end 978 :post-blank 1 :post-affiliated 122 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 44 :end 981 :pre-blank 0 :contents-begin 122 :contents-end 980 :robust-begin 124 :robust-end 978 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 44 :title (#("Table of Contents" 0 17 (:parent #24))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 2 :contents-end 17451 :end 17451 :robust-begin 4 :robust-end 17449 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 2 :end 44 :contents-begin 2 :contents-end 43 :robust-begin 2 :robust-end 41 :post-blank 1 :post-affiliated 2 :mode first-section :granularity nil :parent #70) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 2 :end 43 :post-blank 0 :post-affiliated 2 :mode top-comment :granularity nil :parent #73))) #24 (headline (:raw-value "Introduction" :begin 981 :end 1722 :pre-blank 1 :contents-begin 997 :contents-end 1721 :robust-begin 999 :robust-end 1719 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #75))) :mode nil :granularity nil :parent #70) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #75) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #78) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #81)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #81) #("Guix-notes" 0 10 (:parent #85))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #81))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #78) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #82)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #82) #("Guix bioinformatics" 0 19 (:parent #86))) #("and " 0 4 (:parent #82)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #82) #("GNU Guix main" 0 13 (:parent #88))) #(".\n" 0 2 (:parent #82))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #76))) :mode nil :granularity nil :parent #70) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #79))) :mode section :granularity nil :parent #76) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #79) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #82) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #85)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #85) #("here" 0 4 (:parent #89))) #(".\n" 0 2 (:parent #85))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #82) #("If it works you should be able to install a package with\n" 0 57 (:parent #86))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #82)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #80))) :mode nil :granularity nil :parent #76) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #80) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #83) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #86))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #83) #("#+begin" 0 7 (:parent #87)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #87) #("src" 0 3 (:parent #91))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #87)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #87)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #87)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #87)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #87)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #87) #("src" 0 3 (:parent #97))) #("bash\n" 0 5 (:parent #87))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #81))) :mode nil :granularity nil :parent #76) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #81) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #84) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #87)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #87) #("these" 0 5 (:parent #91))) #("steps carefully.\n" 0 17 (:parent #87))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #82))) :mode nil :granularity nil :parent #76) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #82) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #85) #("#+begin" 0 7 (:parent #88)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #88) #("src" 0 3 (:parent #92))) #("bash\nenv GUIX" 0 13 (:parent #88)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #88) #("PACKAGE" 0 7 (:parent #94))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #88) #("PATH" 0 4 (:parent #95))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #88)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #88) #("src" 0 3 (:parent #97))) #("bash\n" 0 5 (:parent #88))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #85) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #89)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #89)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #89))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #85) #("#+begin" 0 7 (:parent #90)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #90) #("src" 0 3 (:parent #94))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #90))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #85) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #91))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #85) #(" yes\n env GUIX" 0 30 (:parent #92)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #92) #("PACKAGE" 0 7 (:parent #96))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #92) #("PATH" 0 4 (:parent #97))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #92))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #85) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #93))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #85) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #94)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #94) #("PACKAGE" 0 7 (:parent #98))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #94) #("PATH" 0 4 (:parent #99))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #94))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #85) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #95))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #85) #(" which should have the same HASH values " 0 48 (:parent #96)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #96) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #100))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #96)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #96)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #96)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #96)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #96) #("PACKAGE" 0 7 (:parent #106))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #96) #("PATH" 0 4 (:parent #107))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #96)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #96)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #96) #("PACKAGE" 0 7 (:parent #111))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #96) #("PATH" 0 4 (:parent #112))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #96)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #96) #("PACKAGE" 0 7 (:parent #114))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #96) #("PATH" 0 4 (:parent #115))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #96)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #96)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #96)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #96) #("PACKAGE" 0 7 (:parent #121))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #96) #("PATH" 0 4 (:parent #122))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #96)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #96)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #96)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #96)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #96) #("PACKAGE" 0 7 (:parent #128))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #96) #("PATH" 0 4 (:parent #129))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #96)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #96)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #96)))))))) #0)) (plain-list (:type unordered :begin 122 :end 980 :contents-begin 122 :contents-end 980 :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :post-blank 0 :post-affiliated 122 :mode planning :granularity nil :parent #0) (item (:bullet "- " :begin 122 :end 157 :contents-begin 125 :contents-end 157 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil 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:contents-begin 796 :contents-end 831 :post-blank 0 :parent #19) #("ImportError: No module named jinja2" 0 35 (:parent #22))) #("\n" 0 1 (:parent #19)))) (item (:bullet "- " :begin 834 :end 932 :contents-begin 839 :contents-end 932 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 834 :tag nil :mode item :granularity nil :parent #13) (paragraph (:begin 839 :end 932 :contents-begin 839 :contents-end 932 :post-blank 0 :post-affiliated 839 :mode nil :granularity nil :parent #17) (link (:type "custom-id" :path 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(932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 932 :tag nil :mode item :granularity nil :parent #13) (paragraph (:begin 937 :end 980 :contents-begin 937 :contents-end 980 :post-blank 0 :post-affiliated 937 :mode nil :granularity nil :parent #18) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 937 :end 979 :contents-begin 959 :contents-end 977 :post-blank 0 :parent #21) #("Can't run a module" 0 18 (:parent #24))) #("\n" 0 1 (:parent #21))))))))) mapconcat(#f(compiled-function (element) #) ((section (:begin 122 :end 981 :contents-begin 122 :contents-end 980 :robust-begin 122 :robust-end 978 :post-blank 1 :post-affiliated 122 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 44 :end 981 :pre-blank 0 :contents-begin 122 :contents-end 980 :robust-begin 124 :robust-end 978 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 44 :title (#("Table of Contents" 0 17 (:parent #25))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 2 :contents-end 17451 :end 17451 :robust-begin 4 :robust-end 17449 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 2 :end 44 :contents-begin 2 :contents-end 43 :robust-begin 2 :robust-end 41 :post-blank 1 :post-affiliated 2 :mode first-section :granularity nil :parent #71) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 2 :end 43 :post-blank 0 :post-affiliated 2 :mode top-comment :granularity nil :parent #74))) #25 (headline (:raw-value "Introduction" :begin 981 :end 1722 :pre-blank 1 :contents-begin 997 :contents-end 1721 :robust-begin 999 :robust-end 1719 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #76))) :mode nil :granularity nil :parent #71) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #76) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #79) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #82)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #82) #("Guix-notes" 0 10 (:parent #86))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #82))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #79) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #83)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #83) #("Guix bioinformatics" 0 19 (:parent #87))) #("and " 0 4 (:parent #83)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #83) #("GNU Guix main" 0 13 (:parent #89))) #(".\n" 0 2 (:parent #83))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #77))) :mode nil :granularity nil :parent #71) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #80))) :mode section :granularity nil :parent #77) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #80) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #83) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #86)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #86) #("here" 0 4 (:parent #90))) #(".\n" 0 2 (:parent #86))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #83) #("If it works you should be able to install a package with\n" 0 57 (:parent #87))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #83)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #81))) :mode nil :granularity nil :parent #77) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #81) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #84) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #87))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #84) #("#+begin" 0 7 (:parent #88)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #88) #("src" 0 3 (:parent #92))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #88)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #88)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #88)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #88)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #88)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #88) #("src" 0 3 (:parent #98))) #("bash\n" 0 5 (:parent #88))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #82))) :mode nil :granularity nil :parent #77) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #82) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #85) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #88)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #88) #("these" 0 5 (:parent #92))) #("steps carefully.\n" 0 17 (:parent #88))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #83))) :mode nil :granularity nil :parent #77) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #83) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #86) #("#+begin" 0 7 (:parent #89)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #89) #("src" 0 3 (:parent #93))) #("bash\nenv GUIX" 0 13 (:parent #89)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #89) #("PACKAGE" 0 7 (:parent #95))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #89) #("PATH" 0 4 (:parent #96))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #89)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #89) #("src" 0 3 (:parent #98))) #("bash\n" 0 5 (:parent #89))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #86) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #90)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #90)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #90))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #86) #("#+begin" 0 7 (:parent #91)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #91) #("src" 0 3 (:parent #95))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #91))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #86) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #92))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #86) #(" yes\n env GUIX" 0 30 (:parent #93)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #93) #("PACKAGE" 0 7 (:parent #97))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #93) #("PATH" 0 4 (:parent #98))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #93))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #86) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #94))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #86) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #95)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #95) #("PACKAGE" 0 7 (:parent #99))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #95) #("PATH" 0 4 (:parent #100))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #95))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #86) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #96))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #86) #(" which should have the same HASH values " 0 48 (:parent #97)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #97) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #101))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #97)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #97)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #97)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #97)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #97)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #97) #("PACKAGE" 0 7 (:parent #107))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #97) #("PATH" 0 4 (:parent #108))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #97)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #97)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #97)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #97) #("PACKAGE" 0 7 (:parent #112))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #97) #("PATH" 0 4 (:parent #113))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #97)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #97) #("PACKAGE" 0 7 (:parent #115))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #97) #("PATH" 0 4 (:parent #116))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #97)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #97)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #97)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #97)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #97)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #97) #("PACKAGE" 0 7 (:parent #122))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #97) #("PATH" 0 4 (:parent #123))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #97)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #97)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #97)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #97)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #97)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #97) #("PACKAGE" 0 7 (:parent #129))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #97) #("PATH" 0 4 (:parent #130))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #97)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #97)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #97)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #97)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #97)))))))) . #0)) (plain-list (:type unordered :begin 122 :end 980 :contents-begin 122 :contents-end 980 :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :post-blank 0 :post-affiliated 122 :mode planning :granularity nil :parent #1) (item (:bullet "- " :begin 122 :end 157 :contents-begin 125 :contents-end 157 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil 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(239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :post-blank 0 :post-affiliated 202 :mode nil :granularity nil :parent #8) (item (:bullet "- " :begin 202 :end 239 :contents-begin 207 :contents-end 239 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #57)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #57) #("Guix-notes" 0 10 (:parent #61))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #57))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #54) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #58)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #58) #("Guix bioinformatics" 0 19 (:parent #62))) #("and " 0 4 (:parent #58)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #58) #("GNU Guix main" 0 13 (:parent #64))) #(".\n" 0 2 (:parent #58))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #52))) :mode nil :granularity nil :parent #46) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #55))) :mode section :granularity nil :parent #52) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #55) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #58) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #61)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #61) #("here" 0 4 (:parent #65))) #(".\n" 0 2 (:parent #61))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #58) #("If it works you should be able to install a package with\n" 0 57 (:parent #62))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #58)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #56))) :mode nil :granularity nil :parent #52) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #56) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #59) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #62))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #59) #("#+begin" 0 7 (:parent #63)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #63) #("src" 0 3 (:parent #67))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #63)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #63)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #63)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #63)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #63)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #63) #("src" 0 3 (:parent #73))) #("bash\n" 0 5 (:parent #63))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #57))) :mode nil :granularity nil :parent #52) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #57) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #60) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #63)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #63) #("these" 0 5 (:parent #67))) #("steps carefully.\n" 0 17 (:parent #63))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #58))) :mode nil :granularity nil :parent #52) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #58) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #61) #("#+begin" 0 7 (:parent #64)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #64) #("src" 0 3 (:parent #68))) #("bash\nenv GUIX" 0 13 (:parent #64)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #64) #("PACKAGE" 0 7 (:parent #70))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #64) #("PATH" 0 4 (:parent #71))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #64)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #64) #("src" 0 3 (:parent #73))) #("bash\n" 0 5 (:parent #64))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #61) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #65)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #65)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #65))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #61) #("#+begin" 0 7 (:parent #66)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #66) #("src" 0 3 (:parent #70))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #66))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #61) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #67))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #61) #(" yes\n env GUIX" 0 30 (:parent #68)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #68) #("PACKAGE" 0 7 (:parent #72))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #68) #("PATH" 0 4 (:parent #73))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #68))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #61) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #69))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #61) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #70)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #70) #("PACKAGE" 0 7 (:parent #74))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #70) #("PATH" 0 4 (:parent #75))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #70))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #61) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #71))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #61) #(" which should have the same HASH values " 0 48 (:parent #72)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #72) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #76))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #72)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #72)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #72)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #72)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #72) #("PACKAGE" 0 7 (:parent #82))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #72) #("PATH" 0 4 (:parent #83))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #72)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #72)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #72) #("PACKAGE" 0 7 (:parent #87))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #72) #("PATH" 0 4 (:parent #88))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #72)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #72) #("PACKAGE" 0 7 (:parent #90))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #72) #("PATH" 0 4 (:parent #91))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #72)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #72)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #72)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #72) #("PACKAGE" 0 7 (:parent #97))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #72) #("PATH" 0 4 (:parent #98))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #72)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #72)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #72)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #72)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #72) #("PACKAGE" 0 7 (:parent #104))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #72) #("PATH" 0 4 (:parent #105))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #72)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #72)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow 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(:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #343) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #346) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #353))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #350) #("GNU Guix main" 0 13 (:parent #356))) #(".\n" 0 2 (:parent #350))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #344))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #347))) :mode section :granularity nil :parent #344) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #347) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #350) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #353)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #353) #("here" 0 4 (:parent #357))) #(".\n" 0 2 (:parent #353))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #350) #("If it works you should be able to install a package with\n" 0 57 (:parent #354))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #350)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #348))) :mode nil :granularity nil :parent #344) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #348) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #351) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #354))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #351) #("#+begin" 0 7 (:parent #355)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #355) #("src" 0 3 (:parent #359))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #355)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #355)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #355)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #355)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #355) #("src" 0 3 (:parent #365))) #("bash\n" 0 5 (:parent #355))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #349))) :mode nil :granularity nil :parent #344) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #349) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #352) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #355)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #355) #("these" 0 5 (:parent #359))) #("steps carefully.\n" 0 17 (:parent #355))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #350))) :mode nil :granularity nil :parent #344) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #350) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #353) #("#+begin" 0 7 (:parent #356)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #356) #("src" 0 3 (:parent #360))) #("bash\nenv GUIX" 0 13 (:parent #356)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #356) #("PACKAGE" 0 7 (:parent #362))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #356) #("PATH" 0 4 (:parent #363))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #356)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #356) #("src" 0 3 (:parent #365))) #("bash\n" 0 5 (:parent #356))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #353) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #357)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #357)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #357))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #353) #("#+begin" 0 7 (:parent #358)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #358) #("src" 0 3 (:parent #362))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #358))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #353) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #359))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #353) #(" yes\n env GUIX" 0 30 (:parent #360)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #360) #("PACKAGE" 0 7 (:parent #364))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #360) #("PATH" 0 4 (:parent #365))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #360))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #353) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #361))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #353) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #362)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #362) #("PACKAGE" 0 7 (:parent #366))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #362) #("PATH" 0 4 (:parent #367))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #362))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #353) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #363))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #353) #(" which should have the same HASH values " 0 48 (:parent #364)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #364) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #368))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #364)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #374))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #375))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #364)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #364)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #379))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #380))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #364)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #382))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #383))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #364)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #389))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #390))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #364)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #364)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #396))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #397))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #364))))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((headline (:raw-value "Table of Contents" :begin 44 :end 981 :pre-blank 0 :contents-begin 122 :contents-end 980 :robust-begin 124 :robust-end 978 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 44 :title (#("Table of Contents" 0 17 (:parent #0))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 2 :contents-end 17451 :end 17451 :robust-begin 4 :robust-end 17449 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 2 :end 44 :contents-begin 2 :contents-end 43 :robust-begin 2 :robust-end 41 :post-blank 1 :post-affiliated 2 :mode first-section :granularity nil :parent #46) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 2 :end 43 :post-blank 0 :post-affiliated 2 :mode top-comment :granularity nil :parent #49))) #0 (headline (:raw-value "Introduction" :begin 981 :end 1722 :pre-blank 1 :contents-begin 997 :contents-end 1721 :robust-begin 999 :robust-end 1719 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #51))) :mode nil :granularity nil :parent #46) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #51) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #54) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #57)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #57) #("Guix-notes" 0 10 (:parent #61))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #57))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #54) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #58)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #58) #("Guix bioinformatics" 0 19 (:parent #62))) #("and " 0 4 (:parent #58)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #58) #("GNU Guix main" 0 13 (:parent #64))) #(".\n" 0 2 (:parent #58))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #52))) :mode nil :granularity nil :parent #46) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #55))) :mode section :granularity nil :parent #52) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #55) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #58) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #61)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #61) #("here" 0 4 (:parent #65))) #(".\n" 0 2 (:parent #61))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #58) #("If it works you should be able to install a package with\n" 0 57 (:parent #62))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #58)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #56))) :mode nil :granularity nil :parent #52) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #56) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #59) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #62))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #59) #("#+begin" 0 7 (:parent #63)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #63) #("src" 0 3 (:parent #67))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #63)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #63)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #63)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #63)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #63)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #63) #("src" 0 3 (:parent #73))) #("bash\n" 0 5 (:parent #63))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #57))) :mode nil :granularity nil :parent #52) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #57) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #60) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #63)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #63) #("these" 0 5 (:parent #67))) #("steps carefully.\n" 0 17 (:parent #63))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #58))) :mode nil :granularity nil :parent #52) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #58) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #61) #("#+begin" 0 7 (:parent #64)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #64) #("src" 0 3 (:parent #68))) #("bash\nenv GUIX" 0 13 (:parent #64)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #64) #("PACKAGE" 0 7 (:parent #70))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #64) #("PATH" 0 4 (:parent #71))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #64)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #64) #("src" 0 3 (:parent #73))) #("bash\n" 0 5 (:parent #64))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #61) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #65)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #65)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #65))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #61) #("#+begin" 0 7 (:parent #66)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #66) #("src" 0 3 (:parent #70))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #66))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #61) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #67))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #61) #(" yes\n env GUIX" 0 30 (:parent #68)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #68) #("PACKAGE" 0 7 (:parent #72))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #68) #("PATH" 0 4 (:parent #73))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #68))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #61) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #69))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #61) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #70)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #70) #("PACKAGE" 0 7 (:parent #74))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #70) #("PATH" 0 4 (:parent #75))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #70))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #61) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #71))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #61) #(" which should have the same HASH values " 0 48 (:parent #72)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #72) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #76))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #72)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #72)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #72)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #72)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #72) #("PACKAGE" 0 7 (:parent #82))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #72) #("PATH" 0 4 (:parent #83))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #72)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #72)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #72) #("PACKAGE" 0 7 (:parent #87))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #72) #("PATH" 0 4 (:parent #88))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #72)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #72) #("PACKAGE" 0 7 (:parent #90))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #72) #("PATH" 0 4 (:parent #91))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #72)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #72)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #72)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #72) #("PACKAGE" 0 7 (:parent #97))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #72) #("PATH" 0 4 (:parent #98))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #72)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #72)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #72)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #72)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #72) #("PACKAGE" 0 7 (:parent #104))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #72) #("PATH" 0 4 (:parent #105))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #72)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #72)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #72)))))))) (section (:begin 122 :end 981 :contents-begin 122 :contents-end 980 :robust-begin 122 :robust-end 978 :post-blank 1 :post-affiliated 122 :mode section :granularity nil :parent #0) (plain-list (:type unordered :begin 122 :end 980 :contents-begin 122 :contents-end 980 :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :post-blank 0 :post-affiliated 122 :mode planning :granularity nil :parent #3) (item (:bullet "- " :begin 122 :end 157 :contents-begin 125 :contents-end 157 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil 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"#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 757 :end 833 :contents-begin 796 :contents-end 831 :post-blank 0 :parent #24) #("ImportError: No module named jinja2" 0 35 (:parent #27))) #("\n" 0 1 (:parent #24)))) (item (:bullet "- " :begin 834 :end 932 :contents-begin 839 :contents-end 932 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 834 :tag nil :mode item :granularity nil :parent #18) (paragraph (:begin 839 :end 932 :contents-begin 839 :contents-end 932 :post-blank 0 :post-affiliated 839 :mode nil :granularity nil :parent #22) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data" :application nil :search-option nil :begin 839 :end 931 :contents-begin 885 :contents-end 929 :post-blank 0 :parent #25) #("ERROR: can not find directory $HOME/gn2" 0 39 (:parent #28)) (subscript (:begin 924 :end 929 :use-brackets-p nil :contents-begin 925 :contents-end 929 :post-blank 0 :parent #28) #("data" 0 4 (:parent #32)))) #("\n" 0 1 (:parent #25)))) (item (:bullet "- " :begin 932 :end 980 :contents-begin 937 :contents-end 980 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 932 :tag nil :mode item :granularity nil :parent #18) (paragraph (:begin 937 :end 980 :contents-begin 937 :contents-end 980 :post-blank 0 :post-affiliated 937 :mode nil :granularity nil :parent #23) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 937 :end 979 :contents-begin 959 :contents-end 977 :post-blank 0 :parent #26) #("Can't run a module" 0 18 (:parent #29))) #("\n" 0 1 (:parent #26))))))))) (headline (:raw-value "Introduction" :begin 981 :end 1722 :pre-blank 1 :contents-begin 997 :contents-end 1721 :robust-begin 999 :robust-end 1719 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #3))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 2 :contents-end 17451 :end 17451 :robust-begin 4 :robust-end 17449 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #3) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #6) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #9)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #9) #("Guix-notes" 0 10 (:parent #13))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #9))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #6) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #10)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #10) #("Guix bioinformatics" 0 19 (:parent #14))) #("and " 0 4 (:parent #10)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #10) #("GNU Guix main" 0 13 (:parent #16))) #(".\n" 0 2 (:parent #10))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #4))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 2 :contents-end 17451 :end 17451 :robust-begin 4 :robust-end 17449 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #7))) :mode section :granularity nil :parent #4) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #7) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #10) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #13)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #13) #("here" 0 4 (:parent #17))) #(".\n" 0 2 (:parent #13))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #10) #("If it works you should be able to install a package with\n" 0 57 (:parent #14))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #10)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #8))) :mode nil :granularity nil :parent #4) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #8) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #11) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #14))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #11) #("#+begin" 0 7 (:parent #15)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #15) #("src" 0 3 (:parent #19))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #15)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #15)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #15)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #15)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #15)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #15) #("src" 0 3 (:parent #25))) #("bash\n" 0 5 (:parent #15))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #9))) :mode nil :granularity nil :parent #4) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #9) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #12) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #15)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #15) #("these" 0 5 (:parent #19))) #("steps carefully.\n" 0 17 (:parent #15))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #10))) :mode nil :granularity nil :parent #4) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #10) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #13) #("#+begin" 0 7 (:parent #16)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #16) #("src" 0 3 (:parent #20))) #("bash\nenv GUIX" 0 13 (:parent #16)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #16) #("PACKAGE" 0 7 (:parent #22))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #16) #("PATH" 0 4 (:parent #23))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #16)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #16) #("src" 0 3 (:parent #25))) #("bash\n" 0 5 (:parent #16))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #13) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #17)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #17)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #17))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #13) #("#+begin" 0 7 (:parent #18)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #18) #("src" 0 3 (:parent #22))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #18))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #13) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #19))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #13) #(" yes\n env GUIX" 0 30 (:parent #20)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #20) #("PACKAGE" 0 7 (:parent #24))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #20) #("PATH" 0 4 (:parent #25))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #20))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #13) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #21))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #13) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #22)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #22) #("PACKAGE" 0 7 (:parent #26))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #22) #("PATH" 0 4 (:parent #27))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #22))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #13) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #23))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #13) #(" which should have the same HASH values " 0 48 (:parent #24)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #24) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #28))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #24)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #24)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #24)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #24)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #24)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #24) #("PACKAGE" 0 7 (:parent #34))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #24) #("PATH" 0 4 (:parent #35))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #24)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #24)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #24)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #24) #("PACKAGE" 0 7 (:parent #39))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #24) #("PATH" 0 4 (:parent #40))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #24)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #24) #("PACKAGE" 0 7 (:parent #42))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #24) #("PATH" 0 4 (:parent #43))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #24)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #24)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #24)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #24)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #24)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #24) #("PACKAGE" 0 7 (:parent #49))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #24) #("PATH" 0 4 (:parent #50))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #24)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #24)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #24)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #24)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #24)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #24) #("PACKAGE" 0 7 (:parent #56))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #24) #("PATH" 0 4 (:parent #57))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #24)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #24)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #24)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #24)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #24))))))) "") org-export-data((org-data (:begin 1 :contents-begin 2 :contents-end 17451 :end 17451 :robust-begin 4 :robust-end 17449 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 2 :end 44 :contents-begin 2 :contents-end 43 :robust-begin 2 :robust-end 41 :post-blank 1 :post-affiliated 2 :mode first-section :granularity nil :parent #0) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 2 :end 43 :post-blank 0 :post-affiliated 2 :mode top-comment :granularity nil :parent #3))) (headline (:raw-value "Table of Contents" :begin 44 :end 981 :pre-blank 0 :contents-begin 122 :contents-end 980 :robust-begin 124 :robust-end 978 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 44 :title (#("Table of Contents" 0 17 (:parent #4))) :mode nil :granularity nil :parent #0) (section (:begin 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:contents-begin 839 :contents-end 932 :post-blank 0 :post-affiliated 839 :mode nil :granularity nil :parent #24) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data" :application nil :search-option nil :begin 839 :end 931 :contents-begin 885 :contents-end 929 :post-blank 0 :parent #27) #("ERROR: can not find directory $HOME/gn2" 0 39 (:parent #30)) (subscript (:begin 924 :end 929 :use-brackets-p nil :contents-begin 925 :contents-end 929 :post-blank 0 :parent #30) #("data" 0 4 (:parent #34)))) #("\n" 0 1 (:parent #27)))) (item (:bullet "- " :begin 932 :end 980 :contents-begin 937 :contents-end 980 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 932 :tag nil :mode item :granularity nil :parent #20) (paragraph (:begin 937 :end 980 :contents-begin 937 :contents-end 980 :post-blank 0 :post-affiliated 937 :mode nil :granularity nil :parent #25) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 937 :end 979 :contents-begin 959 :contents-end 977 :post-blank 0 :parent #28) #("Can't run a module" 0 18 (:parent #31))) #("\n" 0 1 (:parent #28))))))))) (headline (:raw-value "Introduction" :begin 981 :end 1722 :pre-blank 1 :contents-begin 997 :contents-end 1721 :robust-begin 999 :robust-end 1719 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #5))) :mode nil :granularity nil :parent #0) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #5) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #8) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #11)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #11) #("Guix-notes" 0 10 (:parent #15))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #11))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #8) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #12)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #12) #("Guix bioinformatics" 0 19 (:parent #16))) #("and " 0 4 (:parent #12)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #12) #("GNU Guix main" 0 13 (:parent #18))) #(".\n" 0 2 (:parent #12))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #6))) :mode nil :granularity nil :parent #0) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #9))) :mode section :granularity nil :parent #6) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #9) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #12) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #15)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #15) #("here" 0 4 (:parent #19))) #(".\n" 0 2 (:parent #15))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #12) #("If it works you should be able to install a package with\n" 0 57 (:parent #16))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #12)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #10))) :mode nil :granularity nil :parent #6) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #10) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #13) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #16))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #13) #("#+begin" 0 7 (:parent #17)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #17) #("src" 0 3 (:parent #21))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #17)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #17)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #17)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #17)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #17)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #17) #("src" 0 3 (:parent #27))) #("bash\n" 0 5 (:parent #17))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #11))) :mode nil :granularity nil :parent #6) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #11) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #14) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #17)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #17) #("these" 0 5 (:parent #21))) #("steps carefully.\n" 0 17 (:parent #17))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #12))) :mode nil :granularity nil :parent #6) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #12) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #15) #("#+begin" 0 7 (:parent #18)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #18) #("src" 0 3 (:parent #22))) #("bash\nenv GUIX" 0 13 (:parent #18)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #18) #("PACKAGE" 0 7 (:parent #24))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #18) #("PATH" 0 4 (:parent #25))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #18)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #18) #("src" 0 3 (:parent #27))) #("bash\n" 0 5 (:parent #18))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #15) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #19)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #19)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #19))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #15) #("#+begin" 0 7 (:parent #20)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #20) #("src" 0 3 (:parent #24))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #20))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #15) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #21))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #15) #(" yes\n env GUIX" 0 30 (:parent #22)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #22) #("PACKAGE" 0 7 (:parent #26))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #22) #("PATH" 0 4 (:parent #27))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #22))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #15) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #23))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #15) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #24)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #24) #("PACKAGE" 0 7 (:parent #28))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #24) #("PATH" 0 4 (:parent #29))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #24))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #15) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #25))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #15) #(" which should have the same HASH values " 0 48 (:parent #26)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #26) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #30))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #26)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #26)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #26)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #26)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #26)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #26) #("PACKAGE" 0 7 (:parent #36))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #26) #("PATH" 0 4 (:parent #37))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #26)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #26)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #26)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #26) #("PACKAGE" 0 7 (:parent #41))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #26) #("PATH" 0 4 (:parent #42))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #26)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #26) #("PACKAGE" 0 7 (:parent #44))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #26) #("PATH" 0 4 (:parent #45))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #26)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #26)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #26)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #26)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #26)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #26) #("PACKAGE" 0 7 (:parent #51))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #26) #("PATH" 0 4 (:parent #52))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #26)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #26)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #26)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #26)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #26)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #26) #("PACKAGE" 0 7 (:parent #58))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #26) #("PATH" 0 4 (:parent #59))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #26)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #26)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #26)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #26)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #26))))))) (:export-options (body-only) :back-end #s(org-export-backend :name html :parent nil :transcoders ((bold . org-html-bold) (center-block . org-html-center-block) (clock . org-html-clock) (code . org-html-code) (drawer . org-html-drawer) (dynamic-block . org-html-dynamic-block) (entity . org-html-entity) (example-block . org-html-example-block) (export-block . org-html-export-block) (export-snippet . org-html-export-snippet) (fixed-width . org-html-fixed-width) (footnote-reference . org-html-footnote-reference) (headline . org-html-headline) (horizontal-rule . org-html-horizontal-rule) (inline-src-block . org-html-inline-src-block) (inlinetask . org-html-inlinetask) (inner-template . org-html-inner-template) (italic . org-html-italic) (item . org-html-item) (keyword . org-html-keyword) (latex-environment . org-html-latex-environment) (latex-fragment . org-html-latex-fragment) (line-break . org-html-line-break) (link . org-html-link) (node-property . 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980)) :post-blank 0 :post-affiliated 752 :mode nil :granularity nil :parent #354) (item (:bullet "- " :begin 752 :end 834 :contents-begin 757 :contents-end 834 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 752 :tag nil :mode item :granularity nil :parent #358) (paragraph (:begin 757 :end 834 :contents-begin 757 :contents-end 834 :post-blank 0 :post-affiliated 757 :mode nil :granularity nil :parent #361) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link 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:post-affiliated 839 :mode nil :granularity nil :parent #362) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data" :application nil :search-option nil :begin 839 :end 931 :contents-begin 885 :contents-end 929 :post-blank 0 :parent #365) #("ERROR: can not find directory $HOME/gn2" 0 39 (:parent #368)) (subscript (:begin 924 :end 929 :use-brackets-p nil :contents-begin 925 :contents-end 929 :post-blank 0 :parent #368) #("data" 0 4 (:parent #372)))) #("\n" 0 1 (:parent #365)))) (item (:bullet "- " :begin 932 :end 980 :contents-begin 937 :contents-end 980 :checkbox nil :counter nil :structure ((122 1 "- " nil nil nil 157) (157 1 "- " nil nil nil 582) (202 3 "- " nil nil nil 239) (239 3 "- " nil nil nil 310) (310 3 "- " nil nil nil 345) (345 3 "- " nil nil nil 380) (380 3 "- " nil nil nil 407) (407 3 "- " nil nil nil 452) (452 3 "- " nil nil nil 513) (513 3 "- " nil nil nil 582) (582 1 "- " nil nil nil 709) (709 1 "- " nil nil nil 980) (752 3 "- " nil nil nil 834) (834 3 "- " nil nil nil 932) (932 3 "- " nil nil nil 980)) :pre-blank 0 :post-blank 0 :post-affiliated 932 :tag nil :mode item :granularity nil :parent #358) (paragraph (:begin 937 :end 980 :contents-begin 937 :contents-end 980 :post-blank 0 :post-affiliated 937 :mode nil :granularity nil :parent #363) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 937 :end 979 :contents-begin 959 :contents-end 977 :post-blank 0 :parent #366) #("Can't run a module" 0 18 (:parent #369))) #("\n" 0 1 (:parent #366))))))))) (headline (:raw-value "Introduction" :begin 981 :end 1722 :pre-blank 1 :contents-begin 997 :contents-end 1721 :robust-begin 999 :robust-end 1719 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 981 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 997 :end 1722 :contents-begin 997 :contents-end 1721 :robust-begin 997 :robust-end 1719 :post-blank 1 :post-affiliated 997 :mode section :granularity nil :parent #343) (paragraph (:begin 997 :end 1337 :contents-begin 997 :contents-end 1336 :post-blank 1 :post-affiliated 997 :mode planning :granularity nil :parent #346) #("Large system deployments can get very complex. In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also Pjotr's " 0 183 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1180 :end 1254 :contents-begin 1242 :contents-end 1252 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #353))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1337 :end 1721 :contents-begin 1337 :contents-end 1721 :post-blank 0 :post-affiliated 1337 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest" :application nil :search-option nil :begin 1555 :end 1646 :contents-begin 1624 :contents-end 1643 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//github.com/genenetwork/guix/tree/gn-latest" :format bracket :raw-link "https://github.com/genenetwork/guix/tree/gn-latest" :application nil :search-option nil :begin 1650 :end 1719 :contents-begin 1704 :contents-end 1717 :post-blank 0 :parent #350) #("GNU Guix main" 0 13 (:parent #356))) #(".\n" 0 2 (:parent #350))))) (headline (:raw-value "Source deployment" :begin 1722 :end 17451 :pre-blank 0 :contents-begin 1742 :contents-end 17451 :robust-begin 1744 :robust-end 17449 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1722 :title (#("Source deployment" 0 17 (:parent #344))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install guix" :begin 1742 :end 1992 :pre-blank 1 :contents-begin 1759 :contents-end 1991 :robust-begin 1761 :robust-end 1989 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1742 :title (#("Install guix" 0 12 (:parent #347))) :mode section :granularity nil :parent #344) (section (:begin 1759 :end 1992 :contents-begin 1759 :contents-end 1991 :robust-begin 1759 :robust-end 1989 :post-blank 1 :post-affiliated 1759 :mode section :granularity nil :parent #347) (paragraph (:begin 1759 :end 1909 :contents-begin 1759 :contents-end 1908 :post-blank 1 :post-affiliated 1759 :mode planning :granularity nil :parent #350) #("Deploying from source is also straightforward. Install GNU Guix using\na binary tar ball as described " 0 101 (:parent #353)) (link (:type "https" :path "//github.com/pjotrp/guix-notes" :format bracket :raw-link "https://github.com/pjotrp/guix-notes" :application nil :search-option nil :begin 1860 :end 1906 :contents-begin 1900 :contents-end 1904 :post-blank 0 :parent #353) #("here" 0 4 (:parent #357))) #(".\n" 0 2 (:parent #353))) (paragraph (:begin 1909 :end 1967 :contents-begin 1909 :contents-end 1966 :post-blank 1 :post-affiliated 1909 :mode nil :granularity nil :parent #350) #("If it works you should be able to install a package with\n" 0 57 (:parent #354))) (fixed-width (:begin 1967 :end 1991 :value "guix package -i hello" :post-blank 1 :post-affiliated 1967 :mode nil :granularity nil :parent #350)))) (headline (:raw-value "Checkout the git repositories" :begin 1992 :end 2362 :pre-blank 1 :contents-begin 2026 :contents-end 2361 :robust-begin 2028 :robust-end 2359 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1992 :title (#("Checkout the git repositories" 0 29 (:parent #348))) :mode nil :granularity nil :parent #344) (section (:begin 2026 :end 2362 :contents-begin 2026 :contents-end 2361 :robust-begin 2026 :robust-end 2359 :post-blank 1 :post-affiliated 2026 :mode section :granularity nil :parent #348) (paragraph (:begin 2026 :end 2101 :contents-begin 2026 :contents-end 2100 :post-blank 1 :post-affiliated 2026 :mode planning :granularity nil :parent #351) #("Check out the two relevant guix and guix-bioinformatics git\nrepositories:\n" 0 74 (:parent #354))) (paragraph (:begin 2101 :end 2361 :contents-begin 2101 :contents-end 2361 :post-blank 0 :post-affiliated 2101 :mode nil :granularity nil :parent #351) #("#+begin" 0 7 (:parent #355)) (subscript (:begin 2108 :end 2113 :use-brackets-p nil :contents-begin 2109 :contents-end 2112 :post-blank 1 :parent #355) #("src" 0 3 (:parent #359))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-latest " 0 72 (:parent #355)) (link (:type "https" :path "//github.com/genenetwork/guix-bioinformatics" :format plain :raw-link "https://github.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2185 :end 2235 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #("\ngit clone --branch gn-latest --recursive " 0 42 (:parent #355)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 2277 :end 2313 :contents-begin nil :contents-end nil :post-blank 1 :parent #355)) #("guix-gn-latest\ncd guix-gn-latest\n#+end" 0 38 (:parent #355)) (subscript (:begin 2351 :end 2356 :use-brackets-p nil :contents-begin 2352 :contents-end 2355 :post-blank 1 :parent #355) #("src" 0 3 (:parent #365))) #("bash\n" 0 5 (:parent #355))))) (headline (:raw-value "Update guix" :begin 2362 :end 2642 :pre-blank 1 :contents-begin 2378 :contents-end 2641 :robust-begin 2380 :robust-end 2639 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2362 :title (#("Update guix" 0 11 (:parent #349))) :mode nil :granularity nil :parent #344) (section (:begin 2378 :end 2642 :contents-begin 2378 :contents-end 2641 :robust-begin 2378 :robust-end 2639 :post-blank 1 :post-affiliated 2378 :mode section :granularity nil :parent #349) (paragraph (:begin 2378 :end 2641 :contents-begin 2378 :contents-end 2641 :post-blank 0 :post-affiliated 2378 :mode planning :granularity nil :parent #352) #("At some point you may decide to create, install and run a recent\nversion of the guix-daemon by compiling the guix repository. Follow\n" 0 133 (:parent #355)) (link (:type "https" :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 :begin 2511 :end 2624 :contents-begin 2616 :contents-end 2621 :post-blank 1 :parent #355) #("these" 0 5 (:parent #359))) #("steps carefully.\n" 0 17 (:parent #355))))) (headline (:raw-value "Install GN2" :begin 2642 :end 17451 :pre-blank 1 :contents-begin 2658 :contents-end 17451 :robust-begin 2660 :robust-end 17449 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2642 :title (#("Install GN2" 0 11 (:parent #350))) :mode nil :granularity nil :parent #344) (section (:begin 2658 :end 17451 :contents-begin 2658 :contents-end 17451 :robust-begin 2658 :robust-end 17449 :post-blank 0 :post-affiliated 2658 :mode section :granularity nil :parent #350) (paragraph (:begin 2658 :end 2797 :contents-begin 2658 :contents-end 2796 :post-blank 1 :post-affiliated 2658 :mode planning :granularity nil :parent #353) #("#+begin" 0 7 (:parent #356)) (subscript (:begin 2665 :end 2670 :use-brackets-p nil :contents-begin 2666 :contents-end 2669 :post-blank 1 :parent #356) #("src" 0 3 (:parent #360))) #("bash\nenv GUIX" 0 13 (:parent #356)) (subscript (:begin 2683 :end 2691 :use-brackets-p nil :contents-begin 2684 :contents-end 2691 :post-blank 0 :parent #356) #("PACKAGE" 0 7 (:parent #362))) (subscript (:begin 2691 :end 2696 :use-brackets-p nil :contents-begin 2692 :contents-end 2696 :post-blank 0 :parent #356) #("PATH" 0 4 (:parent #363))) #("=../guix-bioinformatics/ ./pre-inst-env \\\n guix package -i genenetwork2 --fallback \n#+end" 0 90 (:parent #356)) (subscript (:begin 2786 :end 2791 :use-brackets-p nil :contents-begin 2787 :contents-end 2790 :post-blank 1 :parent #356) #("src" 0 3 (:parent #365))) #("bash\n" 0 5 (:parent #356))) (paragraph (:begin 2797 :end 3092 :contents-begin 2797 :contents-end 3091 :post-blank 1 :post-affiliated 2797 :mode nil :granularity nil :parent #353) #("Note that you can use the genenetwork.org guix substitute caching\nserver at " 0 76 (:parent #357)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 2873 :end 2906 :contents-begin nil :contents-end nil :post-blank 1 :parent #357)) #("(which speeds up installs\nsignificantly because all packages are pre-built). Here an IRC session\nwhere we installed GN2 from scratch using GNU Guix and a download\nof the test database:\n" 0 185 (:parent #357))) (paragraph (:begin 3092 :end 3654 :contents-begin 3092 :contents-end 3653 :post-blank 1 :post-affiliated 3092 :mode nil :granularity nil :parent #353) #("#+begin" 0 7 (:parent #358)) (subscript (:begin 3099 :end 3103 :use-brackets-p nil :contents-begin 3100 :contents-end 3103 :post-blank 0 :parent #358) #("src" 0 3 (:parent #362))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-latest-guix repo [07:06]\n yep [07:07]\n git log shows \n" 0 550 (:parent #358))) (paragraph (:begin 3654 :end 3744 :contents-begin 3654 :contents-end 3743 :post-blank 1 :post-affiliated 3654 :mode nil :granularity nil :parent #353) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #359))) (paragraph (:begin 3744 :end 3889 :contents-begin 3744 :contents-end 3888 :post-blank 1 :post-affiliated 3744 :mode nil :granularity nil :parent #353) #(" yes\n env GUIX" 0 30 (:parent #360)) (subscript (:begin 3774 :end 3782 :use-brackets-p nil :contents-begin 3775 :contents-end 3782 :post-blank 0 :parent #360) #("PACKAGE" 0 7 (:parent #364))) (subscript (:begin 3782 :end 3787 :use-brackets-p nil :contents-begin 3783 :contents-end 3787 :post-blank 0 :parent #360) #("PATH" 0 4 (:parent #365))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #360))) (paragraph (:begin 3889 :end 4185 :contents-begin 3889 :contents-end 4184 :post-blank 1 :post-affiliated 3889 :mode nil :granularity nil :parent #353) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #361))) (paragraph (:begin 4185 :end 5379 :contents-begin 4185 :contents-end 5378 :post-blank 1 :post-affiliated 4185 :mode nil :granularity nil :parent #353) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild \n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 754 (:parent #362)) (subscript (:begin 4939 :end 4947 :use-brackets-p nil :contents-begin 4940 :contents-end 4947 :post-blank 0 :parent #362) #("PACKAGE" 0 7 (:parent #366))) (subscript (:begin 4947 :end 4952 :use-brackets-p nil :contents-begin 4948 :contents-end 4952 :post-blank 0 :parent #362) #("PATH" 0 4 (:parent #367))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #362))) (paragraph (:begin 5379 :end 5583 :contents-begin 5379 :contents-end 5582 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #353) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #363))) (paragraph (:begin 5583 :end 17451 :contents-begin 5583 :contents-end 17451 :post-blank 0 :post-affiliated 5583 :mode nil :granularity nil :parent #353) #(" which should have the same HASH values " 0 48 (:parent #364)) (italic (:begin 5631 :end 6540 :post-blank 0 :contents-begin 5632 :contents-end 6539 :parent #364) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #368))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 7340 :end 7405 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond \n [07:36]\n lynx " 0 249 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 7654 :end 7687 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dump\n Resource not found: /\n \n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 225 (:parent #364)) (subscript (:begin 7912 :end 7920 :use-brackets-p nil :contents-begin 7913 :contents-end 7920 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #374))) (subscript (:begin 7920 :end 7925 :use-brackets-p nil :contents-begin 7921 :contents-end 7925 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #375))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #364)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 8041 :end 8068 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\"\n \n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 571 (:parent #364)) (subscript (:begin 8639 :end 8647 :use-brackets-p nil :contents-begin 8640 :contents-end 8647 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #379))) (subscript (:begin 8647 :end 8652 :use-brackets-p nil :contents-begin 8648 :contents-end 8652 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #380))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #364)) (subscript (:begin 9311 :end 9319 :use-brackets-p nil :contents-begin 9312 :contents-end 9319 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #382))) (subscript (:begin 9319 :end 9324 :use-brackets-p nil :contents-begin 9320 :contents-end 9324 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #383))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 9438 :end 9470 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n I'll send you the public key and you can paste it as said\n " 0 548 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 10018 :end 10083 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n [08:06]\n alright\n should be in the E-mail [08:09]\n getting it working it kinda nasty since the server gives no feedback\n it works when you see no more in the build list ;) [08:11]\n btw, you can install software in parallel. Guix does that.\n even the same packages\n so keep building ;)\n try and do this with Debian...\n coffee for me [08:12]\n the first build failed [08:15]\n OK, Dennis fixed that one yesterday [08:27]\n the problem is that sometime source tarballs disappear [08:28]\n R is notorious for that\n haha, that's inconvenient..\n well, it is good that Guix catches them\n but we do not cache sources\n binaries are cached - to some degree - so we don't have to rebuild\n those [08:29]\n time to use the guix cache at guix.genenetwork.org\n try and install the key (it is in the E-mail)\n and see what this lists [08:31]\n env GUIX" 0 1156 (:parent #364)) (subscript (:begin 11239 :end 11247 :use-brackets-p nil :contents-begin 11240 :contents-end 11247 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #389))) (subscript (:begin 11247 :end 11252 :use-brackets-p nil :contents-begin 11248 :contents-end 11252 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #390))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2\n --substitute-urls=" 0 104 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 11356 :end 11389 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dry-run\n should be all binary installs\n it's not.. [08:32]\n if I remove --substitute-urls, the list changes, does that mean I\n have the key set up correctly at least? [08:33]\n dunno [08:35]\n how many packages does it want to build?\n should be zero\n four\n Ah, that is OK - those are default profile things\n genenetwork2 is among the ones to be downloaded so [08:36]\n remove --dry-run\n yeah, good sign :)\n we'll still hit a snag, but run it\n should be fast\n doing it [08:37]\n it worked! [08:38]\n I think [08:39]\n heh [08:40]\n you mean it is finished?\n yep\n type genenetwork2\n complains about not being able to connect to the database [08:41]\n last snag :)\n no database\n well, we succeeded in installing a same-byte install of a very\n complex system :) [08:42]\n (always take time to congratulate yourself)\n now we need to install mysql\n hehe :)\n this can be done throug guix or through debian [08:43]\n the latter is a bit easier here, so let's do that\n fun note: you can mix debian and guix\n Follow instructions on [08:44]\n\n " 0 1321 (:parent #364)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :format plain :raw-link "https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server" :application nil :search-option nil :begin 12710 :end 12787 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n apt-get install mysql-common [08:45]\n may do it\n You can also install with guix, but I need to document that\n btw your internet must be fast :) [08:46]\n hehe it is ;)\n when the database is installed [08:48]\n be sure to set the password as instructed [08:50]\n when mysql is set the genenetwork2 command should fire up the web\n server on localhost:5003 [08:58]\n btw my internet is way slower :) [09:00]\n I'm back [09:04]\n fixed router firmware upgrade problem\n unbricking\n tssk [09:07]\n I'll never leave routers to update themselves again [09:08]\n self-brick highway\n Resuming [09:09]\n auto-updates are evil\n always switch them off\n user02: can you install genenetwork like user has done? [09:10]\n pretty well documented here now :)\n Yes I can [09:11]\n Already installed key\n user02: you are getting binary packages only now? [09:13]\n That's the sanest way to go now\n seriously\n everything should be pre-built from guix.genenetwork.org\n you are downloading?\n yes [09:15]\n cool. Maybe an idea to set up a server \n for your own use\n Stuck at downloading preprocesscore\n should not [09:24]\n what does env GUIX" 0 1393 (:parent #364)) (subscript (:begin 14180 :end 14188 :use-brackets-p nil :contents-begin 14181 :contents-end 14188 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #396))) (subscript (:begin 14188 :end 14193 :use-brackets-p nil :contents-begin 14189 :contents-end 14193 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #397))) #("=../guix-bioinformatics/\n ./pre-inst-env guix package -i genenetwork2\n --substitute-urls=\"" 0 106 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14299 :end 14331 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\" --dry-run\n [09:25]\n say for r-prepocesscore\n download or build?\n mine says download [09:26]\n it only lists the derivatives to be built\n nothing else happens [09:27]\n OK, so there is a problem\n your key may not be working\n everything should be listed as 'to be download' [09:28]\n Hmm\n Ah\n I know where I messed up\n where?\n I did add the key\n However\n (I am documenting)\n I did not tell guix to trust it\n yes\n and there is another potential problem\n Remember the documentation on installing guix?\n You have to tell guix to trust the default key [09:29]\n Right?\n So in this case\n read the IRC log\n That step is mandatory\n user01: how are you doing?\n user02:\n " 0 949 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive" :application nil :search-option nil :begin 15280 :end 15368 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n [09:30]\n a little bit left on the db download\n user02: you should see no more building\n user02: another issue may be that you updated r-preprocesscore\n package in guix-buinformatics [09:32]\n all downstream packages will want to rebuild\n no, not really\n It's not even installed\n checkout a branch of the the old version - make sure we are in synch\n should be at\n /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0\n [09:33]\n \n pjotrp: Possibly we should use the archive utility of Guix to do\n deployment to avoid such out-of-sync differences :) [09:34]\n maybe. I did not get archive to update profiles properly [09:37]\n Also it is good that they get to understand guix\n this way\n carved in stone, eh [09:38]\n Yeah, all good [09:39]\n My mistake was skipping the guix archive part\n Can we begin with the install?\n It's telling me of derivatives that will be downloaded [09:40]\n So we're good\n Here goes\n yeeha [09:42]\n pjotrp, where is this guix.genenetwork.org located at?\n Tennessee\n It's...it's....sloooooooowwwwwwwwwwwwww\n not from Europe\n is it downloading at all?\n It should be extended\n Yes...like at 100KB/s [09:43]\n tear-jerker\n Verizon problems\n who's the host?\n I am getting 500Kb/s\n UT\n Guix's servers can run off more than one server, right?\n I'd like to host that particular server here\n For speed\n yes\n Sooner or later\n It will be a necessity [09:45]\n exactly what I am doing - this is our server\n guix.genenetwork.org:8080\n All done installing [09:46]\n what?\n Now the databases\n what do you mean by slow exactly?\n" 0 2083 (:parent #364))))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) org-export-as(html nil nil t nil) org-export-to-buffer(html "*Org HTML Export*" nil nil nil t nil #f(compiled-function () #)) org-html-export-as-html(nil nil nil t) (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (unwind-protect (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer))) (save-current-buffer (set-buffer temp-buffer) (unwind-protect (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer)))) (let ((temp-buffer (generate-new-buffer " *temp*" t))) (save-current-buffer (set-buffer temp-buffer) (unwind-protect (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer))))) eval-buffer(# nil "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el" nil t) #f(compiled-function (buffer file) #)(# "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el") load-with-code-conversion("/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el" "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el" nil t #f(compiled-function (buffer file) #)) command-line--load-script("/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el") command-line-1(("-scriptload" "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el")) command-line() normal-top-level()
generated by cgit v1.2.3 (git 2.46.2) at 2025-02-19 22:59:58 +0000