Error: user-error ("Unable to resolve link: \"introduction\"")
mapbacktrace(#f(compiled-function (evald func args flags) #))
debug-early-backtrace()
debug-early(error (user-error "Unable to resolve link: \"introduction\""))
signal(user-error ("Unable to resolve link: \"introduction\""))
user-error("Unable to resolve link: %S" "introduction")
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In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (: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 1299 :end 1374 :contents-begin 1361 :contents-end 1371 :post-blank 1 :parent #183) #("Guix-notes" 0 10 (:parent #187))) #("and the main " 0 13 (:parent #183)) (link (:type "fuzzy" :path "README.org" :format bracket :raw-link "README.org" :application nil :search-option nil :begin 1387 :end 1402 :contents-begin nil :contents-end nil :post-blank 1 :parent #183)) #("doc).\n" 0 6 (:parent #183))))) (headline (:raw-value "Binary deployment through GNU Guix" :begin 1409 :end 6537 :pre-blank 0 :contents-begin 1446 :contents-end 6536 :robust-begin 1448 :robust-end 6534 :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 1409 :title (#("Binary deployment through GNU Guix" 0 34 (:parent #178))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Quick installation recipe" :begin 1446 :end 1927 :pre-blank 1 :contents-begin 1476 :contents-end 1926 :robust-begin 1478 :robust-end 1924 :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 1446 :title (#("Quick installation recipe" 0 25 (:parent #181))) :mode section :granularity nil :parent #178) (section (:begin 1476 :end 1927 :contents-begin 1476 :contents-end 1926 :robust-begin 1476 :robust-end 1924 :post-blank 1 :post-affiliated 1476 :mode section :granularity nil :parent #181) (paragraph (:begin 1476 :end 1785 :contents-begin 1476 :contents-end 1784 :post-blank 1 :post-affiliated 1476 :mode planning :granularity nil :parent #184) #("This is a recipe for quick and dirty installation of GN2. For\nconvenience everything is installed as root, though in reality only\nGNU Guix has to be installed as root. I tested this recipe on a fresh\ninstall of Debian 8.3.0 (in KVM) though it should work on any modern\nLinux distribution (including CentOS).\n" 0 308 (:parent #187))) (paragraph (:begin 1785 :end 1926 :contents-begin 1785 :contents-end 1926 :post-blank 0 :post-affiliated 1785 :mode nil :granularity nil :parent #184) #("Note that GN2 consists of an approx. 5 GB installation including\ndatabase. If you use a virtual machine we recommend to use at least\ndouble.\n" 0 141 (:parent #188))))) (headline (:raw-value "Step 1: Install GNU Guix" :begin 1927 :end 3554 :pre-blank 1 :contents-begin 1956 :contents-end 3553 :robust-begin 1958 :robust-end 3551 :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 1927 :title (#("Step 1: Install GNU Guix" 0 24 (:parent #182))) :mode nil :granularity nil :parent #178) (section (:begin 1956 :end 3554 :contents-begin 1956 :contents-end 3553 :robust-begin 1956 :robust-end 3551 :post-blank 1 :post-affiliated 1956 :mode section :granularity nil :parent #182) (paragraph (:begin 1956 :end 2409 :contents-begin 1956 :contents-end 2408 :post-blank 1 :post-affiliated 1956 :mode planning :granularity nil :parent #185) #("Fetch the GNU Guix binary from " 0 31 (:parent #188)) (link (:type "https" :path "//www.gnu.org/software/guix/download/" :format bracket :raw-link "https://www.gnu.org/software/guix/download/" :application nil :search-option nil :begin 1987 :end 2041 :contents-begin 2034 :contents-end 2038 :post-blank 1 :parent #188) #("here" 0 4 (:parent #192))) #("(middle panel) and follow\n" 0 26 (:parent #188)) (link (:type "https" :path "//www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :format bracket :raw-link "https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html" :application nil :search-option nil :begin 2067 :end 2160 :contents-begin 2146 :contents-end 2158 :post-blank 0 :parent #188) #("instructions" 0 12 (:parent #194))) #(". Essentially, download and unpack the tar ball (which\ncreates directories in /gnu and /var/guix), add build users and group\n(Guix builds software as unpriviliged users) and run the Guix daemon\nafter fixing the paths (also known as the 'profile').\n" 0 248 (:parent #188))) (paragraph (:begin 2409 :end 2687 :contents-begin 2409 :contents-end 2686 :post-blank 1 :post-affiliated 2409 :mode nil :granularity nil :parent #185) #("Once you have succeeded, you have to " 0 37 (:parent #189)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key" :application nil :search-option nil :begin 2446 :end 2536 :contents-begin 2522 :contents-end 2533 :post-blank 1 :parent #189) #("set the key" 0 11 (:parent #193))) #("(getting permission\nto download binaries from the GNU server) and you should be able to\ninstall the hello package using binary packages (no building)\n" 0 150 (:parent #189))) (src-block (:language "bash" :switches nil :parameters nil :begin 2687 :end 2795 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "export PATH=~/.guix-profile/bin:$PATH\nguix pull\nguix package -i hello --dry-run\n" :post-blank 1 :post-affiliated 2687 :mode nil :granularity nil :parent #185)) (paragraph (:begin 2795 :end 2829 :contents-begin 2795 :contents-end 2828 :post-blank 1 :post-affiliated 2795 :mode nil :granularity nil :parent #185) #("Which should show something like\n" 0 33 (:parent #191))) (fixed-width (:begin 2829 :end 2939 :value "The following files would be downloaded:\n /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10\n ..." :post-blank 1 :post-affiliated 2829 :mode nil :granularity nil :parent #185)) (paragraph (:begin 2939 :end 2950 :contents-begin 2939 :contents-end 2949 :post-blank 1 :post-affiliated 2939 :mode nil :granularity nil :parent #185) #("#+end" 0 5 (:parent #193)) (subscript (:begin 2944 :end 2948 :use-brackets-p nil :contents-begin 2945 :contents-end 2948 :post-blank 0 :parent #193) #("src" 0 3 (:parent #197))) #("\n" 0 1 (:parent #193))) (paragraph (:begin 2950 :end 3021 :contents-begin 2950 :contents-end 3020 :post-blank 1 :post-affiliated 2950 :mode nil :granularity nil :parent #185) #("means binary installs. The actual installation command of 'hello' is\n" 0 70 (:parent #194))) (src-block (:language "bash" :switches nil :parameters nil :begin 3021 :end 3093 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "guix package -i hello\nhello\n Hello, world!\n" :post-blank 1 :post-affiliated 3021 :mode nil :granularity nil :parent #185)) (paragraph (:begin 3093 :end 3280 :contents-begin 3093 :contents-end 3279 :post-blank 1 :post-affiliated 3093 :mode nil :granularity nil :parent #185) #("If you actually see things building it means that Guix is not yet\nproperly installed and up-to-date, i.e., the key is missing or you\nneed to do a 'guix pull'. Press Ctrl-C to interrupt.\n" 0 186 (:parent #196))) (paragraph (:begin 3280 :end 3553 :contents-begin 3280 :contents-end 3553 :post-blank 0 :post-affiliated 3280 :mode nil :granularity nil :parent #185) #("If you need more help we have another writeup in " 0 49 (:parent #197)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation" :application nil :search-option nil :begin 3329 :end 3425 :contents-begin 3413 :contents-end 3423 :post-blank 0 :parent #197) #("guix-notes" 0 10 (:parent #201))) #(". To get\nrid of the locale warning see " 0 39 (:parent #197)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale" :application nil :search-option nil :begin 3464 :end 3551 :contents-begin 3539 :contents-end 3549 :post-blank 0 :parent #197) #("set-locale" 0 10 (:parent #203))) #(".\n" 0 2 (:parent #197))))) (headline (:raw-value "Step 2: Checkout the GN2 git repositories" :begin 3554 :end 4208 :pre-blank 1 :contents-begin 3600 :contents-end 4207 :robust-begin 3602 :robust-end 4205 :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 3554 :title (#("Step 2: Checkout the GN2 git repositories" 0 41 (:parent #183))) :mode nil :granularity nil :parent #178) (section (:begin 3600 :end 4208 :contents-begin 3600 :contents-end 4207 :robust-begin 3600 :robust-end 4205 :post-blank 1 :post-affiliated 3600 :mode section :granularity nil :parent #183) (paragraph (:begin 3600 :end 3720 :contents-begin 3600 :contents-end 3719 :post-blank 1 :post-affiliated 3600 :mode planning :granularity nil :parent #186) #("To fixate the software dependency graph GN2 uses git repositories of\nGuix packages. First install git if it is missing\n" 0 119 (:parent #189))) (src-block (:language "bash" :switches nil :parameters nil :begin 3720 :end 3825 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "guix package -i git\nexport GIT_SSL_CAINFO=/etc/ssl/certs/ca-certificates.crt\n" :post-blank 1 :post-affiliated 3720 :mode nil :granularity nil :parent #186)) (paragraph (:begin 3825 :end 3876 :contents-begin 3825 :contents-end 3875 :post-blank 1 :post-affiliated 3825 :mode nil :granularity nil :parent #186) #("check out the git repositories (gn-deploy branch)\n" 0 50 (:parent #191))) (paragraph (:begin 3876 :end 4137 :contents-begin 3876 :contents-end 4136 :post-blank 1 :post-affiliated 3876 :mode nil :granularity nil :parent #186) #("#+begin" 0 7 (:parent #192)) (subscript (:begin 3883 :end 3888 :use-brackets-p nil :contents-begin 3884 :contents-end 3887 :post-blank 1 :parent #192) #("src" 0 3 (:parent #196))) #("bash\ncd ~\nmkdir genenetwork\ncd genenetwork\ngit clone --branch gn-deploy " 0 72 (:parent #192)) (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 3960 :end 4010 :contents-begin nil :contents-end nil :post-blank 0 :parent #192)) #("\ngit clone --branch gn-deploy --recursive " 0 42 (:parent #192)) (link (:type "https" :path "//github.com/genenetwork/guix" :format plain :raw-link "https://github.com/genenetwork/guix" :application nil :search-option nil :begin 4052 :end 4088 :contents-begin nil :contents-end nil :post-blank 1 :parent #192)) #("guix-gn-deploy\ncd guix-gn-deploy\n#+end" 0 38 (:parent #192)) (subscript (:begin 4126 :end 4131 :use-brackets-p nil :contents-begin 4127 :contents-end 4130 :post-blank 1 :parent #192) #("src" 0 3 (:parent #202))) #("bash\n" 0 5 (:parent #192))) (paragraph (:begin 4137 :end 4175 :contents-begin 4137 :contents-end 4174 :post-blank 1 :post-affiliated 4137 :mode nil :granularity nil :parent #186) #("To test whether this is working try:\n" 0 37 (:parent #193))) (paragraph (:begin 4175 :end 4207 :contents-begin 4175 :contents-end 4207 :post-blank 0 :post-affiliated 4175 :mode nil :granularity nil :parent #186) #("#+begin" 0 7 (:parent #194)) (subscript (:begin 4182 :end 4187 :use-brackets-p nil :contents-begin 4183 :contents-end 4186 :post-blank 1 :parent #194) #("src" 0 3 (:parent #198))) #("bash\n#+end" 0 10 (:parent #194)) (subscript (:begin 4197 :end 4202 :use-brackets-p nil :contents-begin 4198 :contents-end 4201 :post-blank 1 :parent #194) #("src" 0 3 (:parent #200))) #("bash\n" 0 5 (:parent #194))))) (headline (:raw-value "Step 3: Authorize the GN Guix server" :begin 4208 :end 4659 :pre-blank 1 :contents-begin 4249 :contents-end 4658 :robust-begin 4251 :robust-end 4656 :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 4208 :title (#("Step 3: Authorize the GN Guix server" 0 36 (:parent #184))) :mode nil :granularity nil :parent #178) (section (:begin 4249 :end 4659 :contents-begin 4249 :contents-end 4658 :robust-begin 4249 :robust-end 4656 :post-blank 1 :post-affiliated 4249 :mode section :granularity nil :parent #184) (paragraph (:begin 4249 :end 4349 :contents-begin 4249 :contents-end 4348 :post-blank 1 :post-affiliated 4249 :mode planning :granularity nil :parent #187) #("GN2 has its own GNU Guix binary distribution server. To trust it you have\nto add the following key\n" 0 99 (:parent #190))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4349 :end 4493 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #11217788B41ADC8D5B8E71BD87EF699C65312EC387752899FE9C888856F5C769#)\n )\n)\n" :post-blank 1 :post-affiliated 4349 :mode nil :granularity nil :parent #187)) (paragraph (:begin 4493 :end 4525 :contents-begin 4493 :contents-end 4524 :post-blank 1 :post-affiliated 4493 :mode nil :granularity nil :parent #187) #("by pasting it into the command\n" 0 31 (:parent #192))) (src-block (:language "bash" :switches nil :parameters nil :begin 4525 :end 4578 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "guix archive --authorize\n" :post-blank 1 :post-affiliated 4525 :mode nil :granularity nil :parent #187)) (paragraph (:begin 4578 :end 4595 :contents-begin 4578 :contents-end 4594 :post-blank 1 :post-affiliated 4578 :mode nil :granularity nil :parent #187) #("and hit Ctrl-D.\n" 0 16 (:parent #194))) (paragraph (:begin 4595 :end 4658 :contents-begin 4595 :contents-end 4658 :post-blank 0 :post-affiliated 4595 :mode nil :granularity nil :parent #187) #("Now you can use the substitute server to install GN2 binaries.\n" 0 63 (:parent #195))))) (headline (:raw-value "Step 4: Install and run GN2" :begin 4659 :end 6537 :pre-blank 1 :contents-begin 4691 :contents-end 6536 :robust-begin 4693 :robust-end 6534 :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 4659 :title (#("Step 4: Install and run GN2" 0 27 (:parent #185))) :mode nil :granularity nil :parent #178) (section (:begin 4691 :end 6537 :contents-begin 4691 :contents-end 6536 :robust-begin 4691 :robust-end 6534 :post-blank 1 :post-affiliated 4691 :mode section :granularity nil :parent #185) (paragraph (:begin 4691 :end 4831 :contents-begin 4691 :contents-end 4830 :post-blank 1 :post-affiliated 4691 :mode planning :granularity nil :parent #188) #("Since this is a quick and dirty install we are going to override the\nGNU Guix package path by pointing the package path to our repository:\n" 0 139 (:parent #191))) (src-block (:language "bash" :switches nil :parameters nil :begin 4831 :end 4950 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "rm /root/.config/guix/latest\nln -s ~/genenetwork/guix-gn-deploy/ /root/.config/guix/latest\n" :post-blank 1 :post-affiliated 4831 :mode nil :granularity nil :parent #188)) (paragraph (:begin 4950 :end 5003 :contents-begin 4950 :contents-end 5002 :post-blank 1 :post-affiliated 4950 :mode nil :granularity nil :parent #188) #("Now check whether you can find the GN2 package with\n" 0 52 (:parent #193))) (src-block (:language "bash" :switches nil :parameters nil :begin 5003 :end 5193 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ guix package -A genenetwork2\n genenetwork2 2.0-a8fcff4 out gn/packages/genenetwork.scm:144:2\n" :post-blank 1 :post-affiliated 5003 :mode nil :granularity nil :parent #188)) (paragraph (:begin 5193 :end 5302 :contents-begin 5193 :contents-end 5301 :post-blank 1 :post-affiliated 5193 :mode nil :granularity nil :parent #188) #("(ignore the source file newer then ... messages, this is caused by the\n" 0 71 (:parent #195)) (italic (:begin 5264 :end 5270 :post-blank 0 :contents-begin 5265 :contents-end 5269 :parent #195) #("root" 0 4 (:parent #199))) #(".config/guix/latest override).\n" 0 31 (:parent #195))) (paragraph (:begin 5302 :end 5320 :contents-begin 5302 :contents-end 5319 :post-blank 1 :post-affiliated 5302 :mode nil :granularity nil :parent #188) #("And install with\n" 0 17 (:parent #196))) (src-block (:language "bash" :switches nil :parameters nil :begin 5320 :end 5490 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ \\\n guix package -i genenetwork2 \\\n --substitute-urls=\"http://guix.genenetwork.org\"\n" :post-blank 1 :post-affiliated 5320 :mode nil :granularity nil :parent #188)) (paragraph (:begin 5490 :end 5633 :contents-begin 5490 :contents-end 5632 :post-blank 1 :post-affiliated 5490 :mode nil :granularity nil :parent #188) #("Note: the order of the substitute url's may make a difference in speed\n(put the one first that is fastest for your location and time of day).\n" 0 142 (:parent #198))) (paragraph (:begin 5633 :end 5829 :contents-begin 5633 :contents-end 5828 :post-blank 1 :post-affiliated 5633 :mode nil :granularity nil :parent #188) #("Note: if your system starts building or gives an error it may well be\nStep 3 did not succeed. The installation should actually be smooth at\nthis point and only do binary installs (no compiling).\n" 0 195 (:parent #199))) (paragraph (:begin 5829 :end 5960 :contents-begin 5829 :contents-end 5959 :post-blank 1 :post-affiliated 5829 :mode nil :granularity nil :parent #188) #("After installation you should be able to run genenetwork2 after updating\nthe Guix suggested environment vars. Check the output of\n" 0 130 (:parent #200))) (src-block (:language "bash" :switches nil :parameters nil :begin 5960 :end 6139 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "guix package --search-paths\nexport PYTHONPATH=\"/root/.guix-profile/lib/python3.8/site-packages\"\nexport R_LIBS_SITE=\"/root/.guix-profile/site-library/\"\n" :post-blank 1 :post-affiliated 5960 :mode nil :granularity nil :parent #188)) (paragraph (:begin 6139 :end 6208 :contents-begin 6139 :contents-end 6207 :post-blank 1 :post-affiliated 6139 :mode nil :granularity nil :parent #188) #("and copy-paste the listed exports into the terminal before running:\n" 0 68 (:parent #202))) (src-block (:language "bash" :switches nil :parameters nil :begin 6208 :end 6249 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "genenetwork2\n" :post-blank 1 :post-affiliated 6208 :mode nil :granularity nil :parent #188)) (paragraph (:begin 6249 :end 6500 :contents-begin 6249 :contents-end 6499 :post-blank 1 :post-affiliated 6249 :mode nil :granularity nil :parent #188) #("It will complain that the database is missing. See the next section on\nrunning MySQL server for downloading and installing a MySQL GN2\ndatabase. After installing the database restart genenetwork2 and point\nyour browser at " 0 222 (:parent #204)) (link (:type "http" :path "//localhost:5003/" :format bracket :raw-link "http://localhost:5003/" :application nil :search-option nil :begin 6471 :end 6497 :contents-begin nil :contents-end nil :post-blank 0 :parent #204)) #(".\n" 0 2 (:parent #204))) (paragraph (:begin 6500 :end 6536 :contents-begin 6500 :contents-end 6536 :post-blank 0 :post-affiliated 6500 :mode nil :granularity nil :parent #188) #("End of the GN2 installation recipe!\n" 0 36 (:parent #205)))))) (headline (:raw-value "From source deployment" :begin 6537 :end 7800 :pre-blank 1 :contents-begin 6563 :contents-end 7799 :robust-begin 6565 :robust-end 7797 :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 6537 :title (#("From source deployment" 0 22 (:parent #179))) :mode nil :granularity nil :parent #172) (section (:begin 6563 :end 7800 :contents-begin 6563 :contents-end 7799 :robust-begin 6563 :robust-end 7797 :post-blank 1 :post-affiliated 6563 :mode section :granularity nil :parent #179) (paragraph (:begin 6563 :end 6744 :contents-begin 6563 :contents-end 6743 :post-blank 1 :post-affiliated 6563 :mode planning :granularity nil :parent #182) #("GNU Guix allows for " 0 20 (:parent #185)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 6583 :end 6678 :contents-begin 6652 :contents-end 6675 :post-blank 1 :parent #185) #("reproducible deployment" 0 23 (:parent #189))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #185))) (src-block (:language "sh" :switches nil :parameters nil :begin 6744 :end 6939 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir genenetwork\ncd genenetwork\ngit checkout https://github.com/genenetwork/guix.git gn-stable-guix\ngit checkout https://github.com/genenetwork/guix-bioinformatics.git\n" :post-blank 1 :post-affiliated 6744 :mode nil :granularity nil :parent #182)) (paragraph (:begin 6939 :end 7115 :contents-begin 6939 :contents-end 7114 :post-blank 1 :post-affiliated 6939 :mode nil :granularity nil :parent #182) #("Next build guix (and run) following the instructions in " 0 56 (:parent #187)) (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 6995 :end 7112 :contents-begin 7100 :contents-end 7110 :post-blank 0 :parent #187) #("guix-notes" 0 10 (:parent #191))) #(".\n" 0 2 (:parent #187))) (paragraph (:begin 7115 :end 7179 :contents-begin 7115 :contents-end 7178 :post-blank 1 :post-affiliated 7115 :mode nil :granularity nil :parent #182) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #188))) (fixed-width (:begin 7179 :end 7235 :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command" :post-blank 2 :post-affiliated 7179 :mode nil :granularity nil :parent #182)) (paragraph (:begin 7235 :end 7239 :contents-begin 7235 :contents-end 7238 :post-blank 1 :post-affiliated 7235 :mode nil :granularity nil :parent #182) #("So\n" 0 3 (:parent #190))) (paragraph (:begin 7239 :end 7626 :contents-begin 7239 :contents-end 7625 :post-blank 1 :post-affiliated 7239 :mode nil :granularity nil :parent #182) #("#+begin" 0 7 (:parent #191)) (subscript (:begin 7246 :end 7251 :use-brackets-p nil :contents-begin 7247 :contents-end 7250 :post-blank 1 :parent #191) #("src" 0 3 (:parent #195))) #("sh :lang bash\n#+begin" 0 23 (:parent #191)) (subscript (:begin 7274 :end 7279 :use-brackets-p nil :contents-begin 7275 :contents-end 7278 :post-blank 1 :parent #191) #("src" 0 3 (:parent #197))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #191)) (subscript (:begin 7319 :end 7327 :use-brackets-p nil :contents-begin 7320 :contents-end 7327 :post-blank 0 :parent #191) #("PACKAGE" 0 7 (:parent #199))) (subscript (:begin 7327 :end 7332 :use-brackets-p nil :contents-begin 7328 :contents-end 7332 :post-blank 0 :parent #191) #("PATH" 0 4 (:parent #200))) #("=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork\ngenenetwork1 1.0-d622c803b out ../guix-bioinformatics/gn/packages/bioinformatics.scm:163:2\ngenenetwork2 2.0-9e9475053 out ../guix-bioinformatics/gn/packages/bioinformatics.scm:215:2\n#+end" 0 272 (:parent #191)) (subscript (:begin 7604 :end 7609 :use-brackets-p nil :contents-begin 7605 :contents-end 7608 :post-blank 1 :parent #191) #("src" 0 3 (:parent #202))) #("sh :lang bash\n" 0 16 (:parent #191))) (paragraph (:begin 7626 :end 7640 :contents-begin 7626 :contents-end 7639 :post-blank 1 :post-affiliated 7626 :mode nil :granularity nil :parent #182) #("Install with\n" 0 13 (:parent #192))) (paragraph (:begin 7640 :end 7799 :contents-begin 7640 :contents-end 7799 :post-blank 0 :post-affiliated 7640 :mode nil :granularity nil :parent #182) #("#+begin" 0 7 (:parent #193)) (subscript (:begin 7647 :end 7652 :use-brackets-p nil :contents-begin 7648 :contents-end 7651 :post-blank 1 :parent #193) #("src" 0 3 (:parent #197))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #193)) (subscript (:begin 7692 :end 7700 :use-brackets-p nil :contents-begin 7693 :contents-end 7700 :post-blank 0 :parent #193) #("PACKAGE" 0 7 (:parent #199))) (subscript (:begin 7700 :end 7705 :use-brackets-p nil :contents-begin 7701 :contents-end 7705 :post-blank 0 :parent #193) #("PATH" 0 4 (:parent #200))) #("=../guix-bioinformatics ./pre-inst-env guix package -i genenetwork2\n#+end" 0 73 (:parent #193)) (subscript (:begin 7778 :end 7783 :use-brackets-p nil :contents-begin 7779 :contents-end 7782 :post-blank 1 :parent #193) #("src" 0 3 (:parent #202))) #("sh :lang bash\n" 0 16 (:parent #193))))) (headline (:raw-value "Create archive" :begin 7800 :end 7965 :pre-blank 1 :contents-begin 7818 :contents-end 7963 :robust-begin 7820 :robust-end 7961 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7800 :title (#("Create archive" 0 14 (:parent #180))) :mode nil :granularity nil :parent #172) (section (:begin 7818 :end 7965 :contents-begin 7818 :contents-end 7963 :robust-begin 7818 :robust-end 7961 :post-blank 2 :post-affiliated 7818 :mode section :granularity nil :parent #180) (fixed-width (:begin 7818 :end 7963 :value "env GUIX_PACKAGE_PATH=../../genenetwork/guix-bioinformatics/ ./pre-inst-env guix archive --export -r genenetwork2 > guix_gn2-2.0-9e9475053.nar" :post-blank 1 :post-affiliated 7818 :mode planning :granularity nil :parent #183)))) (headline (:raw-value "Source deployment" :begin 7965 :end 11633 :pre-blank 1 :contents-begin 7986 :contents-end 11632 :robust-begin 7988 :robust-end 11630 :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 7965 :title (#("Source deployment" 0 17 (:parent #181))) :mode nil :granularity nil :parent #172) (section (:begin 7986 :end 8405 :contents-begin 7986 :contents-end 8403 :robust-begin 7986 :robust-end 8401 :post-blank 2 :post-affiliated 7986 :mode section :granularity nil :parent #181) (paragraph (:begin 7986 :end 8067 :contents-begin 7986 :contents-end 8066 :post-blank 1 :post-affiliated 7986 :mode planning :granularity nil :parent #184) #("This section gives a more elaborate instruction for installing GN2\nfrom source.\n" 0 80 (:parent #187))) (paragraph (:begin 8067 :end 8097 :contents-begin 8067 :contents-end 8096 :post-blank 1 :post-affiliated 8067 :mode nil :granularity nil :parent #184) #("First execute above 4 steps:\n" 0 29 (:parent #188))) (plain-list (:type unordered :begin 8097 :end 8403 :contents-begin 8097 :contents-end 8403 :structure ((8097 3 "- " nil nil nil 8157) (8157 3 "- " nil nil nil 8251) (8251 3 "- " nil nil nil 8335) (8335 3 "- " nil nil nil 8403)) :post-blank 0 :post-affiliated 8097 :mode nil :granularity nil :parent #184) (item (:bullet "- " :begin 8097 :end 8157 :contents-begin 8102 :contents-end 8157 :checkbox nil :counter nil :structure ((8097 3 "- " nil nil nil 8157) (8157 3 "- " nil nil nil 8251) (8251 3 "- " nil nil nil 8335) (8335 3 "- " nil nil nil 8403)) :pre-blank 0 :post-blank 0 :post-affiliated 8097 :tag nil :mode item :granularity nil :parent #189) (paragraph (:begin 8102 :end 8157 :contents-begin 8102 :contents-end 8157 :post-blank 0 :post-affiliated 8102 :mode nil :granularity nil :parent #192) (link (:type "custom-id" :path "step-1-install-gnu-guix" :format bracket :raw-link "#step-1-install-gnu-guix" :application nil :search-option nil :begin 8102 :end 8156 :contents-begin 8130 :contents-end 8154 :post-blank 0 :parent #195) #("Step 1: Install GNU Guix" 0 24 (:parent #198))) #("\n" 0 1 (:parent #195)))) (item (:bullet "- " :begin 8157 :end 8251 :contents-begin 8162 :contents-end 8251 :checkbox nil :counter nil :structure ((8097 3 "- " nil nil nil 8157) (8157 3 "- " nil nil nil 8251) (8251 3 "- " nil nil nil 8335) (8335 3 "- " nil nil nil 8403)) :pre-blank 0 :post-blank 0 :post-affiliated 8157 :tag nil :mode item :granularity nil :parent #189) (paragraph (:begin 8162 :end 8251 :contents-begin 8162 :contents-end 8251 :post-blank 0 :post-affiliated 8162 :mode nil :granularity nil :parent #193) (link (:type "custom-id" :path "step-2-checkout-the-gn2-git-repositories" :format bracket :raw-link "#step-2-checkout-the-gn2-git-repositories" :application nil :search-option nil :begin 8162 :end 8250 :contents-begin 8207 :contents-end 8248 :post-blank 0 :parent #196) #("Step 2: Checkout the GN2 git repositories" 0 41 (:parent #199))) #("\n" 0 1 (:parent #196)))) (item (:bullet "- " :begin 8251 :end 8335 :contents-begin 8256 :contents-end 8335 :checkbox nil :counter nil :structure ((8097 3 "- " nil nil nil 8157) (8157 3 "- " nil nil nil 8251) (8251 3 "- " nil nil nil 8335) (8335 3 "- " nil nil nil 8403)) :pre-blank 0 :post-blank 0 :post-affiliated 8251 :tag nil :mode item :granularity nil :parent #189) (paragraph (:begin 8256 :end 8335 :contents-begin 8256 :contents-end 8335 :post-blank 0 :post-affiliated 8256 :mode nil :granularity nil :parent #194) (link (:type "custom-id" :path "step-3-authorize-the-gn-guix-server" :format bracket :raw-link "#step-3-authorize-the-gn-guix-server" :application nil :search-option nil :begin 8256 :end 8334 :contents-begin 8296 :contents-end 8332 :post-blank 0 :parent #197) #("Step 3: Authorize the GN Guix server" 0 36 (:parent #200))) #("\n" 0 1 (:parent #197)))) (item (:bullet "- " :begin 8335 :end 8403 :contents-begin 8340 :contents-end 8403 :checkbox nil :counter nil :structure ((8097 3 "- " nil nil nil 8157) (8157 3 "- " nil nil nil 8251) (8251 3 "- " nil nil nil 8335) (8335 3 "- " nil nil nil 8403)) :pre-blank 0 :post-blank 0 :post-affiliated 8335 :tag nil :mode item :granularity nil :parent #189) (paragraph (:begin 8340 :end 8403 :contents-begin 8340 :contents-end 8403 :post-blank 0 :post-affiliated 8340 :mode nil :granularity nil :parent #195) (link (:type "custom-id" :path "step-4-install-and-run-gn2-" :format bracket :raw-link "#step-4-install-and-run-gn2-" :application nil :search-option nil :begin 8340 :end 8402 :contents-begin 8372 :contents-end 8400 :post-blank 0 :parent #198) #("Step 4: Install and run GN2 " 0 28 (:parent #201))) #("\n" 0 1 (:parent #198)))))) (headline (:raw-value "Run your own copy of GN2" :begin 8405 :end 9515 :pre-blank 1 :contents-begin 8434 :contents-end 9514 :robust-begin 8436 :robust-end 9512 :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 8405 :title (#("Run your own copy of GN2" 0 24 (:parent #185))) :mode nil :granularity nil :parent #181) (section (:begin 8434 :end 9515 :contents-begin 8434 :contents-end 9514 :robust-begin 8434 :robust-end 9512 :post-blank 1 :post-affiliated 8434 :mode section :granularity nil :parent #185) (paragraph (:begin 8434 :end 8632 :contents-begin 8434 :contents-end 8631 :post-blank 1 :post-affiliated 8434 :mode planning :granularity nil :parent #188) #("At some point you may want to fix the source code. Assuming you have\nGuix and Genenetwork2 installed (as described above) clone the GN2\nrepository from " 0 152 (:parent #191)) (link (:type "https" :path "//github.com/genenetwork/genenetwork2" :format plain :raw-link "https://github.com/genenetwork/genenetwork2" :application nil :search-option nil :begin 8586 :end 8629 :contents-begin nil :contents-end nil :post-blank 0 :parent #191)) #(".\n" 0 2 (:parent #191))) (paragraph (:begin 8632 :end 8757 :contents-begin 8632 :contents-end 8756 :post-blank 1 :post-affiliated 8632 :mode nil :granularity nil :parent #188) #("Copy-paste the paths into your terminal (mainly so PYTHON" 0 57 (:parent #192)) (subscript (:begin 8689 :end 8695 :use-brackets-p nil :contents-begin 8690 :contents-end 8694 :post-blank 1 :parent #192) #("PATH" 0 4 (:parent #196))) #("and\nR" 0 5 (:parent #192)) (subscript (:begin 8700 :end 8705 :use-brackets-p nil :contents-begin 8701 :contents-end 8705 :post-blank 0 :parent #192) #("LIBS" 0 4 (:parent #198))) (subscript (:begin 8705 :end 8711 :use-brackets-p nil :contents-begin 8706 :contents-end 8710 :post-blank 1 :parent #192) #("SITE" 0 4 (:parent #199))) #("are set) from the information given by guix:\n" 0 45 (:parent #192))) (fixed-width (:begin 8757 :end 8788 :value "guix package --search-paths" :post-blank 2 :post-affiliated 8757 :mode nil :granularity nil :parent #188)) (paragraph (:begin 8788 :end 8812 :contents-begin 8788 :contents-end 8811 :post-blank 1 :post-affiliated 8788 :mode nil :granularity nil :parent #188) #("Inside the repository:\n" 0 23 (:parent #194))) (fixed-width (:begin 8812 :end 8852 :value "cd genenetwork2\n./bin/genenetwork2" :post-blank 2 :post-affiliated 8812 :mode nil :granularity nil :parent #188)) (paragraph (:begin 8852 :end 9096 :contents-begin 8852 :contents-end 9095 :post-blank 1 :post-affiliated 8852 :mode nil :granularity nil :parent #188) #("Will fire up your local repo " 0 29 (:parent #196)) (link (:type "http" :path "//localhost:5003/" :format plain :raw-link "http://localhost:5003/" :application nil :search-option nil :begin 8881 :end 8904 :contents-begin nil :contents-end nil :post-blank 1 :parent #196)) #("using the\nsettings in ./etc/default" 0 35 (:parent #196)) (subscript (:begin 8939 :end 8951 :use-brackets-p nil :contents-begin 8940 :contents-end 8951 :post-blank 0 :parent #196) #("settings.py" 0 11 (:parent #202))) #(". These settings may\nnot reflect your system. To override settings create your own from a copy of\ndefault" 0 105 (:parent #196)) (subscript (:begin 9056 :end 9069 :use-brackets-p nil :contents-begin 9057 :contents-end 9068 :post-blank 1 :parent #196) #("settings.py" 0 11 (:parent #204))) #("and pass it into GN2 with\n" 0 26 (:parent #196))) (fixed-width (:begin 9096 :end 9139 :value "./bin/genenetwork2 $HOME/my_settings.py" :post-blank 2 :post-affiliated 9096 :mode nil :granularity nil :parent #188)) (paragraph (:begin 9139 :end 9285 :contents-begin 9139 :contents-end 9284 :post-blank 1 :post-affiliated 9139 :mode nil :granularity nil :parent #188) #("and everything " 0 15 (:parent #198)) (bold (:begin 9154 :end 9163 :post-blank 1 :contents-begin 9155 :contents-end 9161 :parent #198) #("should" 0 6 (:parent #202))) #("work (note the full path to the settings\nfile). This way we develop against the exact same dependency graph of\nsoftware.\n" 0 121 (:parent #198))) (paragraph (:begin 9285 :end 9413 :contents-begin 9285 :contents-end 9412 :post-blank 1 :post-affiliated 9285 :mode nil :granularity nil :parent #188) #("If something is not working, take a hint from the settings file\nthat comes in the Guix installation. It sits in something like\n" 0 127 (:parent #199))) (fixed-width (:begin 9413 :end 9514 :value "cat ~/.guix-profile/lib/python3.8/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py" :post-blank 1 :post-affiliated 9413 :mode nil :granularity nil :parent #188)))) (headline (:raw-value "Set up nginx port forwarding" :begin 9515 :end 11633 :pre-blank 1 :contents-begin 9548 :contents-end 11632 :robust-begin 9550 :robust-end 11630 :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 9515 :title (#("Set up nginx port forwarding" 0 28 (:parent #186))) :mode nil :granularity nil :parent #181) (section (:begin 9548 :end 11633 :contents-begin 9548 :contents-end 11632 :robust-begin 9548 :robust-end 11630 :post-blank 1 :post-affiliated 9548 :mode section :granularity nil :parent #186) (paragraph (:begin 9548 :end 9716 :contents-begin 9548 :contents-end 9715 :post-blank 1 :post-affiliated 9548 :mode planning :granularity nil :parent #189) #("nginx can be used as a reverse proxy for GN2. For example, we want to\nexpose GN2 on port 80 while it is running on port 5003. Essentially\nthe configuration looks like\n" 0 167 (:parent #192))) (paragraph (:begin 9716 :end 9856 :contents-begin 9716 :contents-end 9855 :post-blank 1 :post-affiliated 9716 :mode nil :granularity nil :parent #189) #("#+begin" 0 7 (:parent #193)) (subscript (:begin 9723 :end 9728 :use-brackets-p nil :contents-begin 9724 :contents-end 9727 :post-blank 1 :parent #193) #("src" 0 3 (:parent #197))) #("js\n server {\n listen 80;\n server" 0 49 (:parent #193)) (subscript (:begin 9777 :end 9783 :use-brackets-p nil :contents-begin 9778 :contents-end 9782 :post-blank 1 :parent #193) #("name" 0 4 (:parent #199))) #("test-gn2.genenetwork.org;\n access" 0 40 (:parent #193)) (subscript (:begin 9823 :end 9829 :use-brackets-p nil :contents-begin 9824 :contents-end 9827 :post-blank 2 :parent #193) #("log" 0 3 (:parent #201))) #("logs/test-gn2.access.log;\n" 0 26 (:parent #193))) (paragraph (:begin 9856 :end 10025 :contents-begin 9856 :contents-end 10024 :post-blank 1 :post-affiliated 9856 :mode nil :granularity nil :parent #189) #(" proxy" 0 13 (:parent #194)) (subscript (:begin 9869 :end 9877 :use-brackets-p nil :contents-begin 9870 :contents-end 9877 :post-blank 0 :parent #194) #("connect" 0 7 (:parent #198))) (subscript (:begin 9877 :end 9892 :use-brackets-p nil :contents-begin 9878 :contents-end 9885 :post-blank 7 :parent #194) #("timeout" 0 7 (:parent #199))) #("3000;\n proxy" 0 19 (:parent #194)) (subscript (:begin 9911 :end 9916 :use-brackets-p nil :contents-begin 9912 :contents-end 9916 :post-blank 0 :parent #194) #("send" 0 4 (:parent #201))) (subscript (:begin 9916 :end 9934 :use-brackets-p nil :contents-begin 9917 :contents-end 9924 :post-blank 10 :parent #194) #("timeout" 0 7 (:parent #202))) #("3000;\n proxy" 0 19 (:parent #194)) (subscript (:begin 9953 :end 9958 :use-brackets-p nil :contents-begin 9954 :contents-end 9958 :post-blank 0 :parent #194) #("read" 0 4 (:parent #204))) (subscript (:begin 9958 :end 9976 :use-brackets-p nil :contents-begin 9959 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:use-brackets-p nil :contents-begin 10417 :contents-end 10420 :post-blank 1 :parent #195) #("src" 0 3 (:parent #228))) #("js\n" 0 3 (:parent #195))) (paragraph (:begin 10425 :end 10464 :contents-begin 10425 :contents-end 10463 :post-blank 1 :post-affiliated 10425 :mode nil :granularity nil :parent #189) #("Install the nginx webserver (as root)\n" 0 38 (:parent #196))) (fixed-width (:begin 10464 :end 10489 :value "guix package -i nginx" :post-blank 2 :post-affiliated 10464 :mode nil :granularity nil :parent #189)) (paragraph (:begin 10489 :end 10570 :contents-begin 10489 :contents-end 10569 :post-blank 1 :post-affiliated 10489 :mode nil :granularity nil :parent #189) #("The nginx example configuration examples can be found in the Guix\nstore through\n" 0 80 (:parent #198))) (fixed-width (:begin 10570 :end 10757 :value "ls -l /root/.guix-profile/sbin/nginx\nlrwxrwxrwx 3 root guixbuild 66 Dec 31 1969 /root/.guix-profile/sbin/nginx -> 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A configuration file for\nGeneNetwork (reverse proxy) port forwarding can be found in the source\nrepository under ./etc/nginx-genenetwork.conf. Copy this file to /etc\n(still as root)\n" 0 226 (:parent #202))) (fixed-width (:begin 11392 :end 11439 :value "cp ./etc/nginx-genenetwork.conf /etc/nginx/" :post-blank 2 :post-affiliated 11392 :mode nil :granularity nil :parent #189)) (paragraph (:begin 11439 :end 11450 :contents-begin 11439 :contents-end 11449 :post-blank 1 :post-affiliated 11439 :mode nil :granularity nil :parent #189) #("Make dirs\n" 0 10 (:parent #204))) (fixed-width (:begin 11450 :end 11484 :value "mkdir -p /var/spool/nginx/logs" :post-blank 2 :post-affiliated 11450 :mode nil :granularity nil :parent #189)) (paragraph (:begin 11484 :end 11495 :contents-begin 11484 :contents-end 11494 :post-blank 1 :post-affiliated 11484 :mode nil :granularity nil :parent #189) #("Add users\n" 0 10 (:parent #206))) (fixed-width (:begin 11495 :end 11531 :value "adduser nobody ; addgroup nobody" :post-blank 2 :post-affiliated 11495 :mode nil :granularity nil :parent #189)) (paragraph (:begin 11531 :end 11542 :contents-begin 11531 :contents-end 11541 :post-blank 1 :post-affiliated 11531 :mode nil :granularity nil :parent #189) #("Run nginx\n" 0 10 (:parent #208))) (fixed-width (:begin 11542 :end 11632 :value "/root/.guix-profile/sbin/nginx -c /etc/nginx/nginx-genenetwork.conf -p /var/spool/nginx" :post-blank 1 :post-affiliated 11542 :mode nil :granularity nil :parent #189))))) (headline (:raw-value "Source deployment and other information on reproducibility" :begin 11633 :end 13382 :pre-blank 1 :contents-begin 11695 :contents-end 13381 :robust-begin 11697 :robust-end 13379 :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 11633 :title (#("Source deployment and other information on reproducibility" 0 58 (:parent #182))) :mode nil :granularity nil :parent #172) (section (:begin 11695 :end 11752 :contents-begin 11695 :contents-end 11751 :robust-begin 11695 :robust-end 11749 :post-blank 1 :post-affiliated 11695 :mode section :granularity nil :parent #182) (paragraph (:begin 11695 :end 11751 :contents-begin 11695 :contents-end 11751 :post-blank 0 :post-affiliated 11695 :mode planning :granularity nil :parent #185) #("See the document " 0 17 (:parent #188)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 11712 :end 11749 :contents-begin nil :contents-end nil :post-blank 0 :parent #188)) #(".\n" 0 2 (:parent #188)))) (headline (:raw-value "Update to recent guix" :begin 11752 :end 12202 :pre-blank 1 :contents-begin 11778 :contents-end 12201 :robust-begin 11780 :robust-end 12199 :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 11752 :title (#("Update to recent guix" 0 21 (:parent #186))) :mode nil :granularity nil :parent #182) (section (:begin 11778 :end 12202 :contents-begin 11778 :contents-end 12201 :robust-begin 11778 :robust-end 12199 :post-blank 1 :post-affiliated 11778 :mode section :granularity nil :parent #186) (paragraph (:begin 11778 :end 11813 :contents-begin 11778 :contents-end 11812 :post-blank 1 :post-affiliated 11778 :mode planning :granularity nil :parent #189) #("We now compile Guix from scratch.\n" 0 34 (:parent #192))) (paragraph (:begin 11813 :end 12088 :contents-begin 11813 :contents-end 12087 :post-blank 1 :post-affiliated 11813 :mode nil :granularity nil :parent #189) #("Create, install and run a recent version of the guix-daemon by\ncompiling the guix repository you have installed with git in\nstep 2. Follow " 0 139 (:parent #193)) (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 11952 :end 12065 :contents-begin 12057 :contents-end 12062 :post-blank 1 :parent #193) #("these" 0 5 (:parent #197))) #("steps carefully after\n" 0 22 (:parent #193))) (fixed-width (:begin 12088 :end 12123 :value "cd ~/genenetwork/guix-gn-deploy" :post-blank 2 :post-affiliated 12088 :mode nil :granularity nil :parent #189)) (paragraph (:begin 12123 :end 12201 :contents-begin 12123 :contents-end 12201 :post-blank 0 :post-affiliated 12123 :mode nil :granularity nil :parent #189) #("Make sure to restart the guix daemon and run guix client from this\ndirectory.\n" 0 78 (:parent #195))))) (headline (:raw-value "Install GN2" :begin 12202 :end 12595 :pre-blank 1 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"https://orgmode.org/org-info.js") (view . "info") (toc . :with-toc) (ftoc . "0") (tdepth . "max") (sdepth . "max") (mouse . "underline") (buttons . "0") (ltoc . "1") (up . :html-link-up) (home . :html-link-home)) :html-infojs-template "\n\n" :html-inline-image-rules (("file" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("http" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("https" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)")) :html-link-org-files-as-html t :html-mathjax-options ((path "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js") (scale 1.0) (align "center") (font "mathjax-modern") (overflow "overflow") (tags "ams") (indent "0em") (multlinewidth "85%") (tagindent ".8em") (tagside "right")) :html-mathjax-template "\n\n\n\n" :html-inline-image-rules (("file" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("http" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("https" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)")) :html-link-org-files-as-html t :html-mathjax-options ((path "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js") (scale 1.0) (align "center") (font "mathjax-modern") (overflow "overflow") (tags "ams") (indent "0em") (multlinewidth "85%") (tagindent ".8em") (tagside "right")) :html-mathjax-template "\n\n\n\n" :html-inline-image-rules (("file" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("http" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("https" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)")) :html-link-org-files-as-html t :html-mathjax-options ((path "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js") (scale 1.0) (align "center") (font "mathjax-modern") (overflow "overflow") (tags "ams") (indent "0em") (multlinewidth "85%") (tagindent ".8em") (tagside "right")) :html-mathjax-template "\n\n\n\n" :html-inline-image-rules (("file" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("http" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("https" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)")) :html-link-org-files-as-html t :html-mathjax-options ((path "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js") (scale 1.0) (align "center") (font "mathjax-modern") (overflow "overflow") (tags "ams") (indent "0em") (multlinewidth "85%") (tagindent ".8em") (tagside "right")) :html-mathjax-template "\n\n\n\n" :html-inline-image-rules (("file" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("http" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("https" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)")) :html-link-org-files-as-html t :html-mathjax-options ((path "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js") (scale 1.0) (align "center") (font "mathjax-modern") (overflow "overflow") (tags "ams") (indent "0em") (multlinewidth "85%") (tagindent ".8em") (tagside "right")) :html-mathjax-template "\n\n\n\n" :html-inline-image-rules (("file" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("http" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("https" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)")) :html-link-org-files-as-html t :html-mathjax-options ((path "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js") (scale 1.0) (align "center") (font "mathjax-modern") (overflow "overflow") (tags "ams") (indent "0em") (multlinewidth "85%") (tagindent ".8em") (tagside "right")) :html-mathjax-template "\n\n\n\n" :html-inline-image-rules (("file" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("http" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("https" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)")) :html-link-org-files-as-html t :html-mathjax-options ((path "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js") (scale 1.0) (align "center") (font "mathjax-modern") (overflow "overflow") (tags "ams") (indent "0em") (multlinewidth "85%") (tagindent ".8em") (tagside "right")) :html-mathjax-template "\n\n
\n
" :html-format-drawer-function #f(compiled-function (name contents) #%s:
\n\n%s\n
\n