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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As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #183))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #180) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #184)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #184) #("here" 0 4 (:parent #188))) #(". This\ndocument will not get into that. It's assumed that you have a working\ndocker setup.\n" 0 91 (:parent #184))) (paragraph (:begin 830 :end 925 :contents-begin 830 :contents-end 925 :post-blank 0 :post-affiliated 830 :mode nil :granularity nil :parent #180) #("The rest of this document outlines how the docker container used in\nthe CI builds was created.\n" 0 95 (:parent #185))))) (headline (:raw-value "Creating the Docker Images" :begin 926 :end 2194 :pre-blank 1 :contents-begin 956 :contents-end 2193 :robust-begin 958 :robust-end 2191 :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 926 :title (#("Creating the Docker Images" 0 26 (:parent #178))) :mode nil :granularity nil :parent #172) (section (:begin 956 :end 2194 :contents-begin 956 :contents-end 2193 :robust-begin 956 :robust-end 2191 :post-blank 1 :post-affiliated 956 :mode section :granularity nil :parent #178) (paragraph (:begin 956 :end 1071 :contents-begin 956 :contents-end 1070 :post-blank 1 :post-affiliated 956 :mode planning :granularity nil :parent #181) #("The general idea is that GUIX is used to generate a set of binaries,\nwhich will be added to a base mariaDB image.\n" 0 114 (:parent #184))) (paragraph (:begin 1071 :end 1117 :contents-begin 1071 :contents-end 1116 :post-blank 1 :post-affiliated 1071 :mode nil :granularity nil :parent #181) #("First create the gn2 tar archive by running:\n" 0 45 (:parent #185))) (src-block (:language "sh" :switches nil :parameters nil :begin 1117 :end 1343 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "env GUIX_PACKAGE_PATH=\"/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules\" \\\n ./pre-inst-env guix pack --no-grafts\\\n -S /gn2-profile=/ \\\n screen genenetwork2\n" :post-blank 1 :post-affiliated 1117 :mode nil :granularity nil :parent #181)) (paragraph (:begin 1343 :end 1387 :contents-begin 1343 :contents-end 1386 :post-blank 1 :post-affiliated 1343 :mode nil :granularity nil :parent #181) #("The output will look something similar to:\n" 0 43 (:parent #187))) (fixed-width (:begin 1387 :end 1454 :value "/gnu/store/x3m77vwaqcwba24p5s4lrb7w2ii16lj9-tarball-pack.tar.gz" :post-blank 2 :post-affiliated 1387 :mode nil :granularity nil :parent #181)) (paragraph (:begin 1454 :end 1640 :contents-begin 1454 :contents-end 1639 :post-blank 1 :post-affiliated 1454 :mode nil :granularity nil :parent #181) #("Now create a folder from which will host the following dockerfile. You\ncan name this file Dockerfile. 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:post-affiliated 276 :mode section :granularity nil :parent #343) (paragraph (:begin 276 :end 600 :contents-begin 276 :contents-end 599 :post-blank 1 :post-affiliated 276 :mode planning :granularity nil :parent #346) #("The CI(Continuous Integration) system for Genenetwork2 uses " 0 60 (:parent #349)) (link (:type "https" :path "//github.com/features/actions" :format bracket :raw-link "https://github.com/features/actions" :application nil :search-option nil :begin 336 :end 391 :contents-begin 375 :contents-end 389 :post-blank 0 :parent #349) #("Github\nActions" 0 14 (:parent #353))) #(". As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #349))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #346) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #350)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #350) #("here" 0 4 (:parent #354))) #(". This\ndocument will not get into that. It's assumed that you have a working\ndocker setup.\n" 0 91 (:parent #350))) (paragraph (:begin 830 :end 925 :contents-begin 830 :contents-end 925 :post-blank 0 :post-affiliated 830 :mode nil :granularity nil :parent #346) #("The rest of this document outlines how the docker container used in\nthe CI builds was created.\n" 0 95 (:parent #351))))) (headline (:raw-value "Creating the Docker Images" :begin 926 :end 2194 :pre-blank 1 :contents-begin 956 :contents-end 2193 :robust-begin 958 :robust-end 2191 :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 926 :title (#("Creating the Docker Images" 0 26 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 956 :end 2194 :contents-begin 956 :contents-end 2193 :robust-begin 956 :robust-end 2191 :post-blank 1 :post-affiliated 956 :mode section :granularity nil :parent #344) (paragraph (:begin 956 :end 1071 :contents-begin 956 :contents-end 1070 :post-blank 1 :post-affiliated 956 :mode planning :granularity nil :parent #347) #("The general idea is that GUIX is used to generate a set of binaries,\nwhich will be added to a base mariaDB image.\n" 0 114 (:parent #350))) (paragraph (:begin 1071 :end 1117 :contents-begin 1071 :contents-end 1116 :post-blank 1 :post-affiliated 1071 :mode nil :granularity nil :parent #347) #("First create the gn2 tar archive by running:\n" 0 45 (:parent #351))) (src-block (:language "sh" :switches nil :parameters nil :begin 1117 :end 1343 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "env GUIX_PACKAGE_PATH=\"/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules\" \\\n ./pre-inst-env guix pack --no-grafts\\\n -S /gn2-profile=/ \\\n screen genenetwork2\n" :post-blank 1 :post-affiliated 1117 :mode nil :granularity nil :parent #347)) (paragraph (:begin 1343 :end 1387 :contents-begin 1343 :contents-end 1386 :post-blank 1 :post-affiliated 1343 :mode nil :granularity nil :parent #347) #("The output will look something similar to:\n" 0 43 (:parent #353))) (fixed-width (:begin 1387 :end 1454 :value "/gnu/store/x3m77vwaqcwba24p5s4lrb7w2ii16lj9-tarball-pack.tar.gz" :post-blank 2 :post-affiliated 1387 :mode nil :granularity nil :parent #347)) (paragraph (:begin 1454 :end 1640 :contents-begin 1454 :contents-end 1639 :post-blank 1 :post-affiliated 1454 :mode nil :granularity nil :parent #347) #("Now create a folder from which will host the following dockerfile. 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Note that mariadb is the base image\nsince it already has mariadb installed for us.\n" 0 185 (:parent #355))) (src-block (:language "conf" :switches nil :parameters nil :begin 1640 :end 1847 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "FROM mariadb:latest\n\nCOPY ./gn2.tar.gz /tmp/gn2.tar.gz\nRUN tar -xzf /tmp/gn2.tar.gz -C / && rm -f /tmp/gn2.tar.gz && \\\n mkdir -p /usr/local/mysql /genotype_files/genotype/json\n" :post-blank 1 :post-affiliated 1640 :mode nil :granularity nil :parent #347)) (paragraph (:begin 1847 :end 1895 :contents-begin 1847 :contents-end 1894 :post-blank 1 :post-affiliated 1847 :mode nil :granularity nil :parent #347) #("Build the image(Note the fullstop at the end):\n" 0 47 (:parent #357))) (fixed-width (:begin 1895 :end 1955 :value "sudo docker build -t genenetwork2:latest -f Dockerfile ." :post-blank 2 :post-affiliated 1895 :mode nil :granularity nil :parent #347)) (paragraph (:begin 1955 :end 2009 :contents-begin 1955 :contents-end 2008 :post-blank 1 :post-affiliated 1955 :mode nil :granularity nil :parent #347) #("To load the image interactively you've just created:\n" 0 53 (:parent #359))) (fixed-width (:begin 2009 :end 2054 :value "docker run -ti \"genenetwork2:latest\" bash" :post-blank 2 :post-affiliated 2009 :mode nil :granularity nil :parent #347)) (paragraph (:begin 2054 :end 2141 :contents-begin 2054 :contents-end 2140 :post-blank 1 :post-affiliated 2054 :mode nil :granularity nil :parent #347) #("Assuming you have a docker instance running, you could always run\ncommands in it e.g:\n" 0 86 (:parent #361))) (fixed-width (:begin 2141 :end 2193 :value "docker run \"genenetwork2:latest\" python --version" :post-blank 1 :post-affiliated 2141 :mode nil :granularity nil :parent #347)))) (headline (:raw-value "Pushing to DockerHub" :begin 2194 :end 2817 :pre-blank 1 :contents-begin 2218 :contents-end 2817 :robust-begin 2220 :robust-end 2815 :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 2194 :title (#("Pushing to DockerHub" 0 20 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2218 :end 2817 :contents-begin 2218 :contents-end 2817 :robust-begin 2218 :robust-end 2815 :post-blank 0 :post-affiliated 2218 :mode section :granularity nil :parent #345) (paragraph (:begin 2218 :end 2325 :contents-begin 2218 :contents-end 2324 :post-blank 1 :post-affiliated 2218 :mode planning :granularity nil :parent #348) #("We use DockerHub to store the docker images from which we use on our\nCI environment using Github Actions.\n" 0 106 (:parent #351))) (paragraph (:begin 2325 :end 2447 :contents-begin 2325 :contents-end 2446 :post-blank 1 :post-affiliated 2325 :mode nil :granularity nil :parent #348) #("To push to dockerhub, first get the image name by running " 0 58 (:parent #352)) (verbatim (:begin 2383 :end 2398 :post-blank 0 :value "docker\nimages" :parent #352)) #(". 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As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #183))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #180) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #184)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #184) #("here" 0 4 (:parent #188))) #(". This\ndocument will not get into that. It's assumed that you have a working\ndocker setup.\n" 0 91 (:parent #184))) (paragraph (:begin 830 :end 925 :contents-begin 830 :contents-end 925 :post-blank 0 :post-affiliated 830 :mode nil :granularity nil :parent #180) #("The rest of this document outlines how the docker container used in\nthe CI builds was created.\n" 0 95 (:parent #185))))) (headline (:raw-value "Creating the Docker Images" :begin 926 :end 2194 :pre-blank 1 :contents-begin 956 :contents-end 2193 :robust-begin 958 :robust-end 2191 :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 926 :title (#("Creating the Docker Images" 0 26 (:parent #178))) :mode nil :granularity nil :parent #172) (section (:begin 956 :end 2194 :contents-begin 956 :contents-end 2193 :robust-begin 956 :robust-end 2191 :post-blank 1 :post-affiliated 956 :mode section :granularity nil :parent #178) (paragraph (:begin 956 :end 1071 :contents-begin 956 :contents-end 1070 :post-blank 1 :post-affiliated 956 :mode planning :granularity nil :parent #181) #("The general idea is that GUIX is used to generate a set of binaries,\nwhich will be added to a base mariaDB image.\n" 0 114 (:parent #184))) (paragraph (:begin 1071 :end 1117 :contents-begin 1071 :contents-end 1116 :post-blank 1 :post-affiliated 1071 :mode nil :granularity nil :parent #181) #("First create the gn2 tar archive by running:\n" 0 45 (:parent #185))) (src-block (:language "sh" :switches nil :parameters nil :begin 1117 :end 1343 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "env GUIX_PACKAGE_PATH=\"/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules\" \\\n ./pre-inst-env guix pack --no-grafts\\\n -S /gn2-profile=/ \\\n screen genenetwork2\n" :post-blank 1 :post-affiliated 1117 :mode nil :granularity nil :parent #181)) (paragraph (:begin 1343 :end 1387 :contents-begin 1343 :contents-end 1386 :post-blank 1 :post-affiliated 1343 :mode nil :granularity nil :parent #181) #("The output will look something similar to:\n" 0 43 (:parent #187))) (fixed-width (:begin 1387 :end 1454 :value "/gnu/store/x3m77vwaqcwba24p5s4lrb7w2ii16lj9-tarball-pack.tar.gz" :post-blank 2 :post-affiliated 1387 :mode nil :granularity nil :parent #181)) (paragraph (:begin 1454 :end 1640 :contents-begin 1454 :contents-end 1639 :post-blank 1 :post-affiliated 1454 :mode nil :granularity nil :parent #181) #("Now create a folder from which will host the following dockerfile. You\ncan name this file Dockerfile. Note that mariadb is the base image\nsince it already has mariadb installed for us.\n" 0 185 (:parent #189))) (src-block (:language "conf" :switches nil :parameters nil :begin 1640 :end 1847 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "FROM mariadb:latest\n\nCOPY ./gn2.tar.gz /tmp/gn2.tar.gz\nRUN tar -xzf /tmp/gn2.tar.gz -C / && rm -f /tmp/gn2.tar.gz && \\\n mkdir -p /usr/local/mysql /genotype_files/genotype/json\n" :post-blank 1 :post-affiliated 1640 :mode nil :granularity nil :parent #181)) (paragraph (:begin 1847 :end 1895 :contents-begin 1847 :contents-end 1894 :post-blank 1 :post-affiliated 1847 :mode nil :granularity nil :parent #181) #("Build the image(Note the fullstop at the end):\n" 0 47 (:parent #191))) (fixed-width (:begin 1895 :end 1955 :value "sudo docker build -t genenetwork2:latest -f Dockerfile ." :post-blank 2 :post-affiliated 1895 :mode nil :granularity nil :parent #181)) (paragraph (:begin 1955 :end 2009 :contents-begin 1955 :contents-end 2008 :post-blank 1 :post-affiliated 1955 :mode nil :granularity nil :parent #181) #("To load the image interactively you've just created:\n" 0 53 (:parent #193))) (fixed-width (:begin 2009 :end 2054 :value "docker run -ti \"genenetwork2:latest\" bash" :post-blank 2 :post-affiliated 2009 :mode nil :granularity nil :parent #181)) (paragraph (:begin 2054 :end 2141 :contents-begin 2054 :contents-end 2140 :post-blank 1 :post-affiliated 2054 :mode nil :granularity nil :parent #181) #("Assuming you have a docker instance running, you could always run\ncommands in it e.g:\n" 0 86 (:parent #195))) (fixed-width (:begin 2141 :end 2193 :value "docker run \"genenetwork2:latest\" python --version" :post-blank 1 :post-affiliated 2141 :mode nil :granularity nil :parent #181)))) (headline (:raw-value "Pushing to DockerHub" :begin 2194 :end 2817 :pre-blank 1 :contents-begin 2218 :contents-end 2817 :robust-begin 2220 :robust-end 2815 :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 2194 :title (#("Pushing to DockerHub" 0 20 (:parent #179))) :mode nil :granularity nil :parent #172) (section (:begin 2218 :end 2817 :contents-begin 2218 :contents-end 2817 :robust-begin 2218 :robust-end 2815 :post-blank 0 :post-affiliated 2218 :mode section :granularity nil :parent #179) (paragraph (:begin 2218 :end 2325 :contents-begin 2218 :contents-end 2324 :post-blank 1 :post-affiliated 2218 :mode planning :granularity nil :parent #182) #("We use DockerHub to store the docker images from which we use on our\nCI environment using Github Actions.\n" 0 106 (:parent #185))) (paragraph (:begin 2325 :end 2447 :contents-begin 2325 :contents-end 2446 :post-blank 1 :post-affiliated 2325 :mode nil :granularity nil :parent #182) #("To push to dockerhub, first get the image name by running " 0 58 (:parent #186)) (verbatim (:begin 2383 :end 2398 :post-blank 0 :value "docker\nimages" :parent #186)) #(". 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As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #184))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #181) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #185)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #185) #("here" 0 4 (:parent #189))) #(". This\ndocument will not get into that. 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As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #162))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #159) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #163)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #163) #("here" 0 4 (:parent #167))) #(". This\ndocument will not get into that. 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As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #157))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #154) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #158)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #158) #("here" 0 4 (:parent #162))) #(". This\ndocument will not get into that. 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:post-affiliated 276 :mode section :granularity nil :parent #343) (paragraph (:begin 276 :end 600 :contents-begin 276 :contents-end 599 :post-blank 1 :post-affiliated 276 :mode planning :granularity nil :parent #346) #("The CI(Continuous Integration) system for Genenetwork2 uses " 0 60 (:parent #349)) (link (:type "https" :path "//github.com/features/actions" :format bracket :raw-link "https://github.com/features/actions" :application nil :search-option nil :begin 336 :end 391 :contents-begin 375 :contents-end 389 :post-blank 0 :parent #349) #("Github\nActions" 0 14 (:parent #353))) #(". As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #349))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #346) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #350)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #350) #("here" 0 4 (:parent #354))) #(". This\ndocument will not get into that. 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As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #157))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #154) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #158)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #158) #("here" 0 4 (:parent #162))) #(". This\ndocument will not get into that. 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As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #137))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #134) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #138)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #138) #("here" 0 4 (:parent #142))) #(". This\ndocument will not get into that. 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:post-affiliated 276 :mode section :granularity nil :parent #343) (paragraph (:begin 276 :end 600 :contents-begin 276 :contents-end 599 :post-blank 1 :post-affiliated 276 :mode planning :granularity nil :parent #346) #("The CI(Continuous Integration) system for Genenetwork2 uses " 0 60 (:parent #349)) (link (:type "https" :path "//github.com/features/actions" :format bracket :raw-link "https://github.com/features/actions" :application nil :search-option nil :begin 336 :end 391 :contents-begin 375 :contents-end 389 :post-blank 0 :parent #349) #("Github\nActions" 0 14 (:parent #353))) #(". As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #349))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #346) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #350)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #350) #("here" 0 4 (:parent #354))) #(". This\ndocument will not get into that. 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As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #138))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #135) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #139)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #139) #("here" 0 4 (:parent #143))) #(". This\ndocument will not get into that. It's assumed that you have a working\ndocker setup.\n" 0 91 (:parent #139))) (paragraph (:begin 830 :end 925 :contents-begin 830 :contents-end 925 :post-blank 0 :post-affiliated 830 :mode nil :granularity nil :parent #135) #("The rest of this document outlines how the docker container used in\nthe CI builds was created.\n" 0 95 (:parent #140))))) (headline (:raw-value "Creating the Docker Images" :begin 926 :end 2194 :pre-blank 1 :contents-begin 956 :contents-end 2193 :robust-begin 958 :robust-end 2191 :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 926 :title (#("Creating the Docker Images" 0 26 (:parent #133))) :mode nil :granularity nil :parent #127) (section (:begin 956 :end 2194 :contents-begin 956 :contents-end 2193 :robust-begin 956 :robust-end 2191 :post-blank 1 :post-affiliated 956 :mode section :granularity nil :parent #133) (paragraph (:begin 956 :end 1071 :contents-begin 956 :contents-end 1070 :post-blank 1 :post-affiliated 956 :mode planning :granularity nil :parent #136) #("The general idea is that GUIX is used to generate a set of binaries,\nwhich will be added to a base mariaDB image.\n" 0 114 (:parent #139))) (paragraph (:begin 1071 :end 1117 :contents-begin 1071 :contents-end 1116 :post-blank 1 :post-affiliated 1071 :mode nil :granularity nil :parent #136) #("First create the gn2 tar archive by running:\n" 0 45 (:parent #140))) (src-block (:language "sh" :switches nil :parameters nil :begin 1117 :end 1343 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "env GUIX_PACKAGE_PATH=\"/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules\" \\\n ./pre-inst-env guix pack --no-grafts\\\n -S /gn2-profile=/ \\\n screen genenetwork2\n" :post-blank 1 :post-affiliated 1117 :mode nil :granularity nil :parent #136)) (paragraph (:begin 1343 :end 1387 :contents-begin 1343 :contents-end 1386 :post-blank 1 :post-affiliated 1343 :mode nil :granularity nil :parent #136) #("The output will look something similar to:\n" 0 43 (:parent #142))) (fixed-width (:begin 1387 :end 1454 :value "/gnu/store/x3m77vwaqcwba24p5s4lrb7w2ii16lj9-tarball-pack.tar.gz" :post-blank 2 :post-affiliated 1387 :mode nil :granularity nil :parent #136)) (paragraph (:begin 1454 :end 1640 :contents-begin 1454 :contents-end 1639 :post-blank 1 :post-affiliated 1454 :mode nil :granularity nil :parent #136) #("Now create a folder from which will host the following dockerfile. You\ncan name this file Dockerfile. Note that mariadb is the base image\nsince it already has mariadb installed for us.\n" 0 185 (:parent #144))) (src-block (:language "conf" :switches nil :parameters nil :begin 1640 :end 1847 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "FROM mariadb:latest\n\nCOPY ./gn2.tar.gz /tmp/gn2.tar.gz\nRUN tar -xzf /tmp/gn2.tar.gz -C / && rm -f /tmp/gn2.tar.gz && \\\n mkdir -p /usr/local/mysql /genotype_files/genotype/json\n" :post-blank 1 :post-affiliated 1640 :mode nil :granularity nil :parent #136)) (paragraph (:begin 1847 :end 1895 :contents-begin 1847 :contents-end 1894 :post-blank 1 :post-affiliated 1847 :mode nil :granularity nil :parent #136) #("Build the image(Note the fullstop at the end):\n" 0 47 (:parent #146))) (fixed-width (:begin 1895 :end 1955 :value "sudo docker build -t genenetwork2:latest -f Dockerfile ." :post-blank 2 :post-affiliated 1895 :mode nil :granularity nil :parent #136)) (paragraph (:begin 1955 :end 2009 :contents-begin 1955 :contents-end 2008 :post-blank 1 :post-affiliated 1955 :mode nil :granularity nil :parent #136) #("To load the image interactively you've just created:\n" 0 53 (:parent #148))) (fixed-width (:begin 2009 :end 2054 :value "docker run -ti \"genenetwork2:latest\" bash" :post-blank 2 :post-affiliated 2009 :mode nil :granularity nil :parent #136)) (paragraph (:begin 2054 :end 2141 :contents-begin 2054 :contents-end 2140 :post-blank 1 :post-affiliated 2054 :mode nil :granularity nil :parent #136) #("Assuming you have a docker instance running, you could always run\ncommands in it e.g:\n" 0 86 (:parent #150))) (fixed-width (:begin 2141 :end 2193 :value "docker run \"genenetwork2:latest\" python --version" :post-blank 1 :post-affiliated 2141 :mode nil :granularity nil :parent #136)))) (headline (:raw-value "Pushing to DockerHub" :begin 2194 :end 2817 :pre-blank 1 :contents-begin 2218 :contents-end 2817 :robust-begin 2220 :robust-end 2815 :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 2194 :title (#("Pushing to DockerHub" 0 20 (:parent #134))) :mode nil :granularity nil :parent #127) (section (:begin 2218 :end 2817 :contents-begin 2218 :contents-end 2817 :robust-begin 2218 :robust-end 2815 :post-blank 0 :post-affiliated 2218 :mode section :granularity nil :parent #134) (paragraph (:begin 2218 :end 2325 :contents-begin 2218 :contents-end 2324 :post-blank 1 :post-affiliated 2218 :mode planning :granularity nil :parent #137) #("We use DockerHub to store the docker images from which we use on our\nCI environment using Github Actions.\n" 0 106 (:parent #140))) (paragraph (:begin 2325 :end 2447 :contents-begin 2325 :contents-end 2446 :post-blank 1 :post-affiliated 2325 :mode nil :granularity nil :parent #137) #("To push to dockerhub, first get the image name by running " 0 58 (:parent #141)) (verbatim (:begin 2383 :end 2398 :post-blank 0 :value "docker\nimages" :parent #141)) #(". Push to dockerhub using a command similar to:\n" 0 48 (:parent #141))) (fixed-width (:begin 2447 :end 2494 :value "docker push bonfacekilz/genenetwork2:latest" :post-blank 2 :post-affiliated 2447 :mode nil :granularity nil :parent #137)) (paragraph (:begin 2494 :end 2537 :contents-begin 2494 :contents-end 2536 :post-blank 1 :post-affiliated 2494 :mode nil :granularity nil :parent #137) #("Right now, we have 2 images on DockerHub:\n" 0 42 (:parent #143))) (plain-list (:type unordered :begin 2537 :end 2817 :contents-begin 2537 :contents-end 2817 :structure ((2537 0 "- " nil nil nil 2701) (2701 0 "- " nil nil nil 2817)) :post-blank 0 :post-affiliated 2537 :mode nil :granularity nil :parent #137) (item (:bullet "- " :begin 2537 :end 2701 :contents-begin 2539 :contents-end 2701 :checkbox nil :counter nil :structure ((2537 0 "- " nil nil nil 2701) (2701 0 "- " nil nil nil 2817)) :pre-blank 0 :post-blank 0 :post-affiliated 2537 :tag nil :mode item :granularity nil :parent #144) (paragraph (:begin 2539 :end 2701 :contents-begin 2539 :contents-end 2701 :post-blank 0 :post-affiliated 2539 :mode nil :granularity nil :parent #147) (link (:type "https" :path "//hub.docker.com/repository/docker/bonfacekilz/python2-genenetwork2" :format plain :raw-link "https://hub.docker.com/repository/docker/bonfacekilz/python2-genenetwork2" :application nil :search-option nil :begin 2539 :end 2612 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #(":\n Contains the python2 version of gn2. Don't use this. Please use the\n python3 image!\n" 0 89 (:parent #150)))) (item (:bullet "- " :begin 2701 :end 2817 :contents-begin 2703 :contents-end 2817 :checkbox nil :counter nil :structure ((2537 0 "- " nil nil nil 2701) (2701 0 "- " nil nil nil 2817)) :pre-blank 0 :post-blank 0 :post-affiliated 2701 :tag nil :mode item :granularity nil :parent #144) (paragraph (:begin 2703 :end 2817 :contents-begin 2703 :contents-end 2817 :post-blank 0 :post-affiliated 2703 :mode nil :granularity nil :parent #148) (link (:type "https" :path "//hub.docker.com/repository/docker/bonfacekilz/python3-genenetwork2" :format plain :raw-link "https://hub.docker.com/repository/docker/bonfacekilz/python3-genenetwork2" :application nil :search-option nil :begin 2703 :end 2776 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #(":\n Contains the python3 version of gn2.\n" 0 41 (:parent #151))))))))) #57)) #33)) . #0)) (paragraph (:begin 115 :end 147 :contents-begin 115 :contents-end 147 :post-blank 0 :post-affiliated 115 :mode nil :granularity nil :parent #1) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 115 :end 146 :contents-begin 132 :contents-end 144 :post-blank 0 :parent #4) #("Introduction" 0 12 (:parent #7))) #("\n" 0 1 (:parent #4)))) (item (:bullet "- " :begin 147 :end 209 :contents-begin 149 :contents-end 209 :checkbox nil :counter nil :structure ((113 0 "- " nil nil nil 147) (147 0 "- " nil nil nil 209) (209 0 "- " nil nil nil 259)) :pre-blank 0 :post-blank 0 :post-affiliated 147 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 113 :end 259 :contents-begin 113 :contents-end 259 :structure ((113 0 "- " nil nil nil 147) (147 0 "- " nil nil nil 209) (209 0 "- " nil nil nil 259)) :post-blank 0 :post-affiliated 113 :mode planning :granularity nil :parent (section (:begin 113 :end 260 :contents-begin 113 :contents-end 259 :robust-begin 113 :robust-end 257 :post-blank 1 :post-affiliated 113 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 35 :end 260 :pre-blank 0 :contents-begin 113 :contents-end 259 :robust-begin 115 :robust-end 257 :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 35 :title (#("Table of Contents" 0 17 (:parent #82))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 2817 :end 2817 :robust-begin 3 :robust-end 2815 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 35 :contents-begin 1 :contents-end 34 :robust-begin 1 :robust-end 32 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #128) (keyword (:key "TITLE" :value "Genenetwork2 Dockerized" :begin 1 :end 34 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #131))) #82 (headline (:raw-value "Introduction" :begin 260 :end 926 :pre-blank 1 :contents-begin 276 :contents-end 925 :robust-begin 278 :robust-end 923 :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 260 :title (#("Introduction" 0 12 (:parent #133))) :mode nil :granularity nil :parent #128) (section (:begin 276 :end 926 :contents-begin 276 :contents-end 925 :robust-begin 276 :robust-end 923 :post-blank 1 :post-affiliated 276 :mode section :granularity nil :parent #133) (paragraph (:begin 276 :end 600 :contents-begin 276 :contents-end 599 :post-blank 1 :post-affiliated 276 :mode planning :granularity nil :parent #136) #("The CI(Continuous Integration) system for Genenetwork2 uses " 0 60 (:parent #139)) (link (:type "https" :path "//github.com/features/actions" :format bracket :raw-link "https://github.com/features/actions" :application nil :search-option nil :begin 336 :end 391 :contents-begin 375 :contents-end 389 :post-blank 0 :parent #139) #("Github\nActions" 0 14 (:parent #143))) #(". As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #139))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #136) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #140)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #140) #("here" 0 4 (:parent #144))) #(". This\ndocument will not get into that. It's assumed that you have a working\ndocker setup.\n" 0 91 (:parent #140))) (paragraph (:begin 830 :end 925 :contents-begin 830 :contents-end 925 :post-blank 0 :post-affiliated 830 :mode nil :granularity nil :parent #136) #("The rest of this document outlines how the docker container used in\nthe CI builds was created.\n" 0 95 (:parent #141))))) (headline (:raw-value "Creating the Docker Images" :begin 926 :end 2194 :pre-blank 1 :contents-begin 956 :contents-end 2193 :robust-begin 958 :robust-end 2191 :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 926 :title (#("Creating the Docker Images" 0 26 (:parent #134))) :mode nil :granularity nil :parent #128) (section (:begin 956 :end 2194 :contents-begin 956 :contents-end 2193 :robust-begin 956 :robust-end 2191 :post-blank 1 :post-affiliated 956 :mode section :granularity nil :parent #134) (paragraph (:begin 956 :end 1071 :contents-begin 956 :contents-end 1070 :post-blank 1 :post-affiliated 956 :mode planning :granularity nil :parent #137) #("The general idea is that GUIX is used to generate a set of binaries,\nwhich will be added to a base mariaDB image.\n" 0 114 (:parent #140))) (paragraph (:begin 1071 :end 1117 :contents-begin 1071 :contents-end 1116 :post-blank 1 :post-affiliated 1071 :mode nil :granularity nil :parent #137) #("First create the gn2 tar archive by running:\n" 0 45 (:parent #141))) (src-block (:language "sh" :switches nil :parameters nil :begin 1117 :end 1343 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "env GUIX_PACKAGE_PATH=\"/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules\" \\\n ./pre-inst-env guix pack --no-grafts\\\n -S /gn2-profile=/ \\\n screen genenetwork2\n" :post-blank 1 :post-affiliated 1117 :mode nil :granularity nil :parent #137)) (paragraph (:begin 1343 :end 1387 :contents-begin 1343 :contents-end 1386 :post-blank 1 :post-affiliated 1343 :mode nil :granularity nil :parent #137) #("The output will look something similar to:\n" 0 43 (:parent #143))) (fixed-width (:begin 1387 :end 1454 :value "/gnu/store/x3m77vwaqcwba24p5s4lrb7w2ii16lj9-tarball-pack.tar.gz" :post-blank 2 :post-affiliated 1387 :mode nil :granularity nil :parent #137)) (paragraph (:begin 1454 :end 1640 :contents-begin 1454 :contents-end 1639 :post-blank 1 :post-affiliated 1454 :mode nil :granularity nil :parent #137) #("Now create a folder from which will host the following dockerfile. You\ncan name this file Dockerfile. Note that mariadb is the base image\nsince it already has mariadb installed for us.\n" 0 185 (:parent #145))) (src-block (:language "conf" :switches nil :parameters nil :begin 1640 :end 1847 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "FROM mariadb:latest\n\nCOPY ./gn2.tar.gz /tmp/gn2.tar.gz\nRUN tar -xzf /tmp/gn2.tar.gz -C / && rm -f /tmp/gn2.tar.gz && \\\n mkdir -p /usr/local/mysql /genotype_files/genotype/json\n" :post-blank 1 :post-affiliated 1640 :mode nil :granularity nil :parent #137)) (paragraph (:begin 1847 :end 1895 :contents-begin 1847 :contents-end 1894 :post-blank 1 :post-affiliated 1847 :mode nil :granularity nil :parent #137) #("Build the image(Note the fullstop at the end):\n" 0 47 (:parent #147))) (fixed-width (:begin 1895 :end 1955 :value "sudo docker build -t genenetwork2:latest -f Dockerfile ." :post-blank 2 :post-affiliated 1895 :mode nil :granularity nil :parent #137)) (paragraph (:begin 1955 :end 2009 :contents-begin 1955 :contents-end 2008 :post-blank 1 :post-affiliated 1955 :mode nil :granularity nil :parent #137) #("To load the image interactively you've just created:\n" 0 53 (:parent #149))) (fixed-width (:begin 2009 :end 2054 :value "docker run -ti \"genenetwork2:latest\" bash" :post-blank 2 :post-affiliated 2009 :mode nil :granularity nil :parent #137)) (paragraph (:begin 2054 :end 2141 :contents-begin 2054 :contents-end 2140 :post-blank 1 :post-affiliated 2054 :mode nil :granularity nil :parent #137) #("Assuming you have a docker instance running, you could always run\ncommands in it e.g:\n" 0 86 (:parent #151))) (fixed-width (:begin 2141 :end 2193 :value "docker run \"genenetwork2:latest\" python --version" :post-blank 1 :post-affiliated 2141 :mode nil :granularity nil :parent #137)))) (headline (:raw-value "Pushing to DockerHub" :begin 2194 :end 2817 :pre-blank 1 :contents-begin 2218 :contents-end 2817 :robust-begin 2220 :robust-end 2815 :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 2194 :title (#("Pushing to DockerHub" 0 20 (:parent #135))) :mode nil :granularity nil :parent #128) (section (:begin 2218 :end 2817 :contents-begin 2218 :contents-end 2817 :robust-begin 2218 :robust-end 2815 :post-blank 0 :post-affiliated 2218 :mode section :granularity nil :parent #135) (paragraph (:begin 2218 :end 2325 :contents-begin 2218 :contents-end 2324 :post-blank 1 :post-affiliated 2218 :mode planning :granularity nil :parent #138) #("We use DockerHub to store the docker images from which we use on our\nCI environment using Github Actions.\n" 0 106 (:parent #141))) (paragraph (:begin 2325 :end 2447 :contents-begin 2325 :contents-end 2446 :post-blank 1 :post-affiliated 2325 :mode nil :granularity nil :parent #138) #("To push to dockerhub, first get the image name by running " 0 58 (:parent #142)) (verbatim (:begin 2383 :end 2398 :post-blank 0 :value "docker\nimages" :parent #142)) #(". Push to dockerhub using a command similar to:\n" 0 48 (:parent #142))) (fixed-width (:begin 2447 :end 2494 :value "docker push bonfacekilz/genenetwork2:latest" :post-blank 2 :post-affiliated 2447 :mode nil :granularity nil :parent #138)) (paragraph (:begin 2494 :end 2537 :contents-begin 2494 :contents-end 2536 :post-blank 1 :post-affiliated 2494 :mode nil :granularity nil :parent #138) #("Right now, we have 2 images on DockerHub:\n" 0 42 (:parent #144))) (plain-list (:type unordered :begin 2537 :end 2817 :contents-begin 2537 :contents-end 2817 :structure ((2537 0 "- " nil nil nil 2701) (2701 0 "- " nil nil nil 2817)) :post-blank 0 :post-affiliated 2537 :mode nil :granularity nil :parent #138) (item (:bullet "- " :begin 2537 :end 2701 :contents-begin 2539 :contents-end 2701 :checkbox nil :counter nil :structure ((2537 0 "- " nil nil nil 2701) (2701 0 "- " nil nil nil 2817)) :pre-blank 0 :post-blank 0 :post-affiliated 2537 :tag nil :mode item :granularity nil :parent #145) (paragraph (:begin 2539 :end 2701 :contents-begin 2539 :contents-end 2701 :post-blank 0 :post-affiliated 2539 :mode nil :granularity nil :parent #148) (link (:type "https" :path "//hub.docker.com/repository/docker/bonfacekilz/python2-genenetwork2" :format plain :raw-link "https://hub.docker.com/repository/docker/bonfacekilz/python2-genenetwork2" :application nil :search-option nil :begin 2539 :end 2612 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #(":\n Contains the python2 version of gn2. Don't use this. 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As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #140))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #137) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #141)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #141) #("here" 0 4 (:parent #145))) #(". This\ndocument will not get into that. It's assumed that you have a working\ndocker setup.\n" 0 91 (:parent #141))) (paragraph (:begin 830 :end 925 :contents-begin 830 :contents-end 925 :post-blank 0 :post-affiliated 830 :mode nil :granularity nil :parent #137) #("The rest of this document outlines how the docker container used in\nthe CI builds was created.\n" 0 95 (:parent #142))))) (headline (:raw-value "Creating the Docker Images" :begin 926 :end 2194 :pre-blank 1 :contents-begin 956 :contents-end 2193 :robust-begin 958 :robust-end 2191 :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 926 :title (#("Creating the Docker Images" 0 26 (:parent #135))) :mode nil :granularity nil :parent #129) (section (:begin 956 :end 2194 :contents-begin 956 :contents-end 2193 :robust-begin 956 :robust-end 2191 :post-blank 1 :post-affiliated 956 :mode section :granularity nil :parent #135) (paragraph (:begin 956 :end 1071 :contents-begin 956 :contents-end 1070 :post-blank 1 :post-affiliated 956 :mode planning :granularity nil :parent #138) #("The general idea is that GUIX is used to generate a set of binaries,\nwhich will be added to a base mariaDB image.\n" 0 114 (:parent #141))) (paragraph (:begin 1071 :end 1117 :contents-begin 1071 :contents-end 1116 :post-blank 1 :post-affiliated 1071 :mode nil :granularity nil :parent #138) #("First create the gn2 tar archive by running:\n" 0 45 (:parent #142))) (src-block (:language "sh" :switches nil :parameters nil :begin 1117 :end 1343 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "env GUIX_PACKAGE_PATH=\"/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules\" \\\n ./pre-inst-env guix pack --no-grafts\\\n -S /gn2-profile=/ \\\n screen genenetwork2\n" :post-blank 1 :post-affiliated 1117 :mode nil :granularity nil :parent #138)) (paragraph (:begin 1343 :end 1387 :contents-begin 1343 :contents-end 1386 :post-blank 1 :post-affiliated 1343 :mode nil :granularity nil :parent #138) #("The output will look something similar to:\n" 0 43 (:parent #144))) (fixed-width (:begin 1387 :end 1454 :value "/gnu/store/x3m77vwaqcwba24p5s4lrb7w2ii16lj9-tarball-pack.tar.gz" :post-blank 2 :post-affiliated 1387 :mode nil :granularity nil :parent #138)) (paragraph (:begin 1454 :end 1640 :contents-begin 1454 :contents-end 1639 :post-blank 1 :post-affiliated 1454 :mode nil :granularity nil :parent #138) #("Now create a folder from which will host the following dockerfile. You\ncan name this file Dockerfile. Note that mariadb is the base image\nsince it already has mariadb installed for us.\n" 0 185 (:parent #146))) (src-block (:language "conf" :switches nil :parameters nil :begin 1640 :end 1847 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "FROM mariadb:latest\n\nCOPY ./gn2.tar.gz /tmp/gn2.tar.gz\nRUN tar -xzf /tmp/gn2.tar.gz -C / && rm -f /tmp/gn2.tar.gz && \\\n mkdir -p /usr/local/mysql /genotype_files/genotype/json\n" :post-blank 1 :post-affiliated 1640 :mode nil :granularity nil :parent #138)) (paragraph (:begin 1847 :end 1895 :contents-begin 1847 :contents-end 1894 :post-blank 1 :post-affiliated 1847 :mode nil :granularity nil :parent #138) #("Build the image(Note the fullstop at the end):\n" 0 47 (:parent #148))) (fixed-width (:begin 1895 :end 1955 :value "sudo docker build -t genenetwork2:latest -f Dockerfile ." :post-blank 2 :post-affiliated 1895 :mode nil :granularity nil :parent #138)) (paragraph (:begin 1955 :end 2009 :contents-begin 1955 :contents-end 2008 :post-blank 1 :post-affiliated 1955 :mode nil :granularity nil :parent #138) #("To load the image interactively you've just created:\n" 0 53 (:parent #150))) (fixed-width (:begin 2009 :end 2054 :value "docker run -ti \"genenetwork2:latest\" bash" :post-blank 2 :post-affiliated 2009 :mode nil :granularity nil :parent #138)) (paragraph (:begin 2054 :end 2141 :contents-begin 2054 :contents-end 2140 :post-blank 1 :post-affiliated 2054 :mode nil :granularity nil :parent #138) #("Assuming you have a docker instance running, you could always run\ncommands in it e.g:\n" 0 86 (:parent #152))) (fixed-width (:begin 2141 :end 2193 :value "docker run \"genenetwork2:latest\" python --version" :post-blank 1 :post-affiliated 2141 :mode nil :granularity nil :parent #138)))) (headline (:raw-value "Pushing to DockerHub" :begin 2194 :end 2817 :pre-blank 1 :contents-begin 2218 :contents-end 2817 :robust-begin 2220 :robust-end 2815 :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 2194 :title (#("Pushing to DockerHub" 0 20 (:parent #136))) :mode nil :granularity nil :parent #129) (section (:begin 2218 :end 2817 :contents-begin 2218 :contents-end 2817 :robust-begin 2218 :robust-end 2815 :post-blank 0 :post-affiliated 2218 :mode section :granularity nil :parent #136) (paragraph (:begin 2218 :end 2325 :contents-begin 2218 :contents-end 2324 :post-blank 1 :post-affiliated 2218 :mode planning :granularity nil :parent #139) #("We use DockerHub to store the docker images from which we use on our\nCI environment using Github Actions.\n" 0 106 (:parent #142))) (paragraph (:begin 2325 :end 2447 :contents-begin 2325 :contents-end 2446 :post-blank 1 :post-affiliated 2325 :mode nil :granularity nil :parent #139) #("To push to dockerhub, first get the image name by running " 0 58 (:parent #143)) (verbatim (:begin 2383 :end 2398 :post-blank 0 :value "docker\nimages" :parent #143)) #(". 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As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #105))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #102) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #106)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #106) #("here" 0 4 (:parent #110))) #(". This\ndocument will not get into that. 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You\ncan name this file Dockerfile. 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You\ncan name this file Dockerfile. 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Push to dockerhub using a command similar to:\n" 0 48 (:parent #84))) (fixed-width (:begin 2447 :end 2494 :value "docker push bonfacekilz/genenetwork2:latest" :post-blank 2 :post-affiliated 2447 :mode nil :granularity nil :parent #80)) (paragraph (:begin 2494 :end 2537 :contents-begin 2494 :contents-end 2536 :post-blank 1 :post-affiliated 2494 :mode nil :granularity nil :parent #80) #("Right now, we have 2 images on DockerHub:\n" 0 42 (:parent #86))) (plain-list (:type unordered :begin 2537 :end 2817 :contents-begin 2537 :contents-end 2817 :structure ((2537 0 "- " nil nil nil 2701) (2701 0 "- " nil nil nil 2817)) :post-blank 0 :post-affiliated 2537 :mode nil :granularity nil :parent #80) (item (:bullet "- " :begin 2537 :end 2701 :contents-begin 2539 :contents-end 2701 :checkbox nil :counter nil :structure ((2537 0 "- " nil nil nil 2701) (2701 0 "- " nil nil nil 2817)) :pre-blank 0 :post-blank 0 :post-affiliated 2537 :tag nil :mode item :granularity nil :parent #87) (paragraph (:begin 2539 :end 2701 :contents-begin 2539 :contents-end 2701 :post-blank 0 :post-affiliated 2539 :mode nil :granularity nil :parent #90) (link (:type "https" :path "//hub.docker.com/repository/docker/bonfacekilz/python2-genenetwork2" :format plain :raw-link "https://hub.docker.com/repository/docker/bonfacekilz/python2-genenetwork2" :application nil :search-option nil :begin 2539 :end 2612 :contents-begin nil :contents-end nil :post-blank 0 :parent #93)) #(":\n Contains the python2 version of gn2. 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:post-affiliated 276 :mode section :granularity nil :parent #343) (paragraph (:begin 276 :end 600 :contents-begin 276 :contents-end 599 :post-blank 1 :post-affiliated 276 :mode planning :granularity nil :parent #346) #("The CI(Continuous Integration) system for Genenetwork2 uses " 0 60 (:parent #349)) (link (:type "https" :path "//github.com/features/actions" :format bracket :raw-link "https://github.com/features/actions" :application nil :search-option nil :begin 336 :end 391 :contents-begin 375 :contents-end 389 :post-blank 0 :parent #349) #("Github\nActions" 0 14 (:parent #353))) #(". As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #349))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #346) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #350)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #350) #("here" 0 4 (:parent #354))) #(". This\ndocument will not get into that. It's assumed that you have a working\ndocker setup.\n" 0 91 (:parent #350))) (paragraph (:begin 830 :end 925 :contents-begin 830 :contents-end 925 :post-blank 0 :post-affiliated 830 :mode nil :granularity nil :parent #346) #("The rest of this document outlines how the docker container used in\nthe CI builds was created.\n" 0 95 (:parent #351))))) (headline (:raw-value "Creating the Docker Images" :begin 926 :end 2194 :pre-blank 1 :contents-begin 956 :contents-end 2193 :robust-begin 958 :robust-end 2191 :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 926 :title (#("Creating the Docker Images" 0 26 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 956 :end 2194 :contents-begin 956 :contents-end 2193 :robust-begin 956 :robust-end 2191 :post-blank 1 :post-affiliated 956 :mode section :granularity nil :parent #344) (paragraph (:begin 956 :end 1071 :contents-begin 956 :contents-end 1070 :post-blank 1 :post-affiliated 956 :mode planning :granularity nil :parent #347) #("The general idea is that GUIX is used to generate a set of binaries,\nwhich will be added to a base mariaDB image.\n" 0 114 (:parent #350))) (paragraph (:begin 1071 :end 1117 :contents-begin 1071 :contents-end 1116 :post-blank 1 :post-affiliated 1071 :mode nil :granularity nil :parent #347) #("First create the gn2 tar archive by running:\n" 0 45 (:parent #351))) (src-block (:language "sh" :switches nil :parameters nil :begin 1117 :end 1343 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "env GUIX_PACKAGE_PATH=\"/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules\" \\\n ./pre-inst-env guix pack --no-grafts\\\n -S /gn2-profile=/ \\\n screen genenetwork2\n" :post-blank 1 :post-affiliated 1117 :mode nil :granularity nil :parent #347)) (paragraph (:begin 1343 :end 1387 :contents-begin 1343 :contents-end 1386 :post-blank 1 :post-affiliated 1343 :mode nil :granularity nil :parent #347) #("The output will look something similar to:\n" 0 43 (:parent #353))) (fixed-width (:begin 1387 :end 1454 :value "/gnu/store/x3m77vwaqcwba24p5s4lrb7w2ii16lj9-tarball-pack.tar.gz" :post-blank 2 :post-affiliated 1387 :mode nil :granularity nil :parent #347)) (paragraph (:begin 1454 :end 1640 :contents-begin 1454 :contents-end 1639 :post-blank 1 :post-affiliated 1454 :mode nil :granularity nil :parent #347) #("Now create a folder from which will host the following dockerfile. You\ncan name this file Dockerfile. Note that mariadb is the base image\nsince it already has mariadb installed for us.\n" 0 185 (:parent #355))) (src-block (:language "conf" :switches nil :parameters nil :begin 1640 :end 1847 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "FROM mariadb:latest\n\nCOPY ./gn2.tar.gz /tmp/gn2.tar.gz\nRUN tar -xzf /tmp/gn2.tar.gz -C / && rm -f /tmp/gn2.tar.gz && \\\n mkdir -p /usr/local/mysql /genotype_files/genotype/json\n" :post-blank 1 :post-affiliated 1640 :mode nil :granularity nil :parent #347)) (paragraph (:begin 1847 :end 1895 :contents-begin 1847 :contents-end 1894 :post-blank 1 :post-affiliated 1847 :mode nil :granularity nil :parent #347) #("Build the image(Note the fullstop at the end):\n" 0 47 (:parent #357))) (fixed-width (:begin 1895 :end 1955 :value "sudo docker build -t genenetwork2:latest -f Dockerfile ." :post-blank 2 :post-affiliated 1895 :mode nil :granularity nil :parent #347)) (paragraph (:begin 1955 :end 2009 :contents-begin 1955 :contents-end 2008 :post-blank 1 :post-affiliated 1955 :mode nil :granularity nil :parent #347) #("To load the image interactively you've just created:\n" 0 53 (:parent #359))) (fixed-width (:begin 2009 :end 2054 :value "docker run -ti \"genenetwork2:latest\" bash" :post-blank 2 :post-affiliated 2009 :mode nil :granularity nil :parent #347)) (paragraph (:begin 2054 :end 2141 :contents-begin 2054 :contents-end 2140 :post-blank 1 :post-affiliated 2054 :mode nil :granularity nil :parent #347) #("Assuming you have a docker instance running, you could always run\ncommands in it e.g:\n" 0 86 (:parent #361))) (fixed-width (:begin 2141 :end 2193 :value "docker run \"genenetwork2:latest\" python --version" :post-blank 1 :post-affiliated 2141 :mode nil :granularity nil :parent #347)))) (headline (:raw-value "Pushing to DockerHub" :begin 2194 :end 2817 :pre-blank 1 :contents-begin 2218 :contents-end 2817 :robust-begin 2220 :robust-end 2815 :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 2194 :title (#("Pushing to DockerHub" 0 20 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2218 :end 2817 :contents-begin 2218 :contents-end 2817 :robust-begin 2218 :robust-end 2815 :post-blank 0 :post-affiliated 2218 :mode section :granularity nil :parent #345) (paragraph (:begin 2218 :end 2325 :contents-begin 2218 :contents-end 2324 :post-blank 1 :post-affiliated 2218 :mode planning :granularity nil :parent #348) #("We use DockerHub to store the docker images from which we use on our\nCI environment using Github Actions.\n" 0 106 (:parent #351))) (paragraph (:begin 2325 :end 2447 :contents-begin 2325 :contents-end 2446 :post-blank 1 :post-affiliated 2325 :mode nil :granularity nil :parent #348) #("To push to dockerhub, first get the image name by running " 0 58 (:parent #352)) (verbatim (:begin 2383 :end 2398 :post-blank 0 :value "docker\nimages" :parent #352)) #(". Push to dockerhub using a command similar to:\n" 0 48 (:parent #352))) (fixed-width (:begin 2447 :end 2494 :value "docker push bonfacekilz/genenetwork2:latest" :post-blank 2 :post-affiliated 2447 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2494 :end 2537 :contents-begin 2494 :contents-end 2536 :post-blank 1 :post-affiliated 2494 :mode nil :granularity nil :parent #348) #("Right now, we have 2 images on DockerHub:\n" 0 42 (:parent #354))) (plain-list (:type unordered :begin 2537 :end 2817 :contents-begin 2537 :contents-end 2817 :structure ((2537 0 "- " nil nil nil 2701) (2701 0 "- " nil nil nil 2817)) :post-blank 0 :post-affiliated 2537 :mode nil :granularity nil :parent #348) (item (:bullet "- " :begin 2537 :end 2701 :contents-begin 2539 :contents-end 2701 :checkbox nil :counter nil :structure ((2537 0 "- " nil nil nil 2701) (2701 0 "- " nil nil nil 2817)) :pre-blank 0 :post-blank 0 :post-affiliated 2537 :tag nil :mode item :granularity nil :parent #355) (paragraph (:begin 2539 :end 2701 :contents-begin 2539 :contents-end 2701 :post-blank 0 :post-affiliated 2539 :mode nil :granularity nil :parent #358) (link (:type "https" :path "//hub.docker.com/repository/docker/bonfacekilz/python2-genenetwork2" :format plain :raw-link "https://hub.docker.com/repository/docker/bonfacekilz/python2-genenetwork2" :application nil :search-option nil :begin 2539 :end 2612 :contents-begin nil :contents-end nil :post-blank 0 :parent #361)) #(":\n Contains the python2 version of gn2. 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As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #81))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #78) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #82)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #82) #("here" 0 4 (:parent #86))) #(". This\ndocument will not get into that. It's assumed that you have a working\ndocker setup.\n" 0 91 (:parent #82))) (paragraph (:begin 830 :end 925 :contents-begin 830 :contents-end 925 :post-blank 0 :post-affiliated 830 :mode nil :granularity nil :parent #78) #("The rest of this document outlines how the docker container used in\nthe CI builds was created.\n" 0 95 (:parent #83))))) (headline (:raw-value "Creating the Docker Images" :begin 926 :end 2194 :pre-blank 1 :contents-begin 956 :contents-end 2193 :robust-begin 958 :robust-end 2191 :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 926 :title (#("Creating the Docker Images" 0 26 (:parent #76))) :mode nil :granularity nil :parent #70) (section (:begin 956 :end 2194 :contents-begin 956 :contents-end 2193 :robust-begin 956 :robust-end 2191 :post-blank 1 :post-affiliated 956 :mode section :granularity nil :parent #76) (paragraph (:begin 956 :end 1071 :contents-begin 956 :contents-end 1070 :post-blank 1 :post-affiliated 956 :mode planning :granularity nil :parent #79) #("The general idea is that GUIX is used to generate a set of binaries,\nwhich will be added to a base mariaDB image.\n" 0 114 (:parent #82))) (paragraph (:begin 1071 :end 1117 :contents-begin 1071 :contents-end 1116 :post-blank 1 :post-affiliated 1071 :mode nil :granularity nil :parent #79) #("First create the gn2 tar archive by running:\n" 0 45 (:parent #83))) (src-block (:language "sh" :switches nil :parameters nil :begin 1117 :end 1343 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "env GUIX_PACKAGE_PATH=\"/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules\" \\\n ./pre-inst-env guix pack --no-grafts\\\n -S /gn2-profile=/ \\\n screen genenetwork2\n" :post-blank 1 :post-affiliated 1117 :mode nil :granularity nil :parent #79)) (paragraph (:begin 1343 :end 1387 :contents-begin 1343 :contents-end 1386 :post-blank 1 :post-affiliated 1343 :mode nil :granularity nil :parent #79) #("The output will look something similar to:\n" 0 43 (:parent #85))) (fixed-width (:begin 1387 :end 1454 :value "/gnu/store/x3m77vwaqcwba24p5s4lrb7w2ii16lj9-tarball-pack.tar.gz" :post-blank 2 :post-affiliated 1387 :mode nil :granularity nil :parent #79)) (paragraph (:begin 1454 :end 1640 :contents-begin 1454 :contents-end 1639 :post-blank 1 :post-affiliated 1454 :mode nil :granularity nil :parent #79) #("Now create a folder from which will host the following dockerfile. 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As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #82))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #79) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #83)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #83) #("here" 0 4 (:parent #87))) #(". This\ndocument will not get into that. 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As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #57))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #54) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #58)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #58) #("here" 0 4 (:parent #62))) #(". This\ndocument will not get into that. It's assumed that you have a working\ndocker setup.\n" 0 91 (:parent #58))) (paragraph (:begin 830 :end 925 :contents-begin 830 :contents-end 925 :post-blank 0 :post-affiliated 830 :mode nil :granularity nil :parent #54) #("The rest of this document outlines how the docker container used in\nthe CI builds was created.\n" 0 95 (:parent #59))))) (headline (:raw-value "Creating the Docker Images" :begin 926 :end 2194 :pre-blank 1 :contents-begin 956 :contents-end 2193 :robust-begin 958 :robust-end 2191 :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 926 :title (#("Creating the Docker Images" 0 26 (:parent #52))) :mode nil :granularity nil :parent #46) (section (:begin 956 :end 2194 :contents-begin 956 :contents-end 2193 :robust-begin 956 :robust-end 2191 :post-blank 1 :post-affiliated 956 :mode section :granularity nil :parent #52) (paragraph (:begin 956 :end 1071 :contents-begin 956 :contents-end 1070 :post-blank 1 :post-affiliated 956 :mode planning :granularity nil :parent #55) #("The general idea is that GUIX is used to generate a set of binaries,\nwhich will be added to a base mariaDB image.\n" 0 114 (:parent #58))) (paragraph (:begin 1071 :end 1117 :contents-begin 1071 :contents-end 1116 :post-blank 1 :post-affiliated 1071 :mode nil :granularity nil :parent #55) #("First create the gn2 tar archive by running:\n" 0 45 (:parent #59))) (src-block (:language "sh" :switches nil :parameters nil :begin 1117 :end 1343 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "env GUIX_PACKAGE_PATH=\"/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules\" \\\n ./pre-inst-env guix pack --no-grafts\\\n -S /gn2-profile=/ \\\n screen genenetwork2\n" :post-blank 1 :post-affiliated 1117 :mode nil :granularity nil :parent #55)) (paragraph (:begin 1343 :end 1387 :contents-begin 1343 :contents-end 1386 :post-blank 1 :post-affiliated 1343 :mode nil :granularity nil :parent #55) #("The output will look something similar to:\n" 0 43 (:parent #61))) (fixed-width (:begin 1387 :end 1454 :value "/gnu/store/x3m77vwaqcwba24p5s4lrb7w2ii16lj9-tarball-pack.tar.gz" :post-blank 2 :post-affiliated 1387 :mode nil :granularity nil :parent #55)) (paragraph (:begin 1454 :end 1640 :contents-begin 1454 :contents-end 1639 :post-blank 1 :post-affiliated 1454 :mode nil :granularity nil :parent #55) #("Now create a folder from which will host the following dockerfile. You\ncan name this file Dockerfile. Note that mariadb is the base image\nsince it already has mariadb installed for us.\n" 0 185 (:parent #63))) (src-block (:language "conf" :switches nil :parameters nil :begin 1640 :end 1847 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "FROM mariadb:latest\n\nCOPY ./gn2.tar.gz /tmp/gn2.tar.gz\nRUN tar -xzf /tmp/gn2.tar.gz -C / && rm -f /tmp/gn2.tar.gz && \\\n mkdir -p /usr/local/mysql /genotype_files/genotype/json\n" :post-blank 1 :post-affiliated 1640 :mode nil :granularity nil :parent #55)) (paragraph (:begin 1847 :end 1895 :contents-begin 1847 :contents-end 1894 :post-blank 1 :post-affiliated 1847 :mode nil :granularity nil :parent #55) #("Build the image(Note the fullstop at the end):\n" 0 47 (:parent #65))) (fixed-width (:begin 1895 :end 1955 :value "sudo docker build -t genenetwork2:latest -f Dockerfile ." :post-blank 2 :post-affiliated 1895 :mode nil :granularity nil :parent #55)) (paragraph (:begin 1955 :end 2009 :contents-begin 1955 :contents-end 2008 :post-blank 1 :post-affiliated 1955 :mode nil :granularity nil :parent #55) #("To load the image interactively you've just created:\n" 0 53 (:parent #67))) (fixed-width (:begin 2009 :end 2054 :value "docker run -ti \"genenetwork2:latest\" bash" :post-blank 2 :post-affiliated 2009 :mode nil :granularity nil :parent #55)) (paragraph (:begin 2054 :end 2141 :contents-begin 2054 :contents-end 2140 :post-blank 1 :post-affiliated 2054 :mode nil :granularity nil :parent #55) #("Assuming you have a docker instance running, you could always run\ncommands in it e.g:\n" 0 86 (:parent #69))) (fixed-width (:begin 2141 :end 2193 :value "docker run \"genenetwork2:latest\" python --version" :post-blank 1 :post-affiliated 2141 :mode nil :granularity nil :parent #55)))) (headline (:raw-value "Pushing to DockerHub" :begin 2194 :end 2817 :pre-blank 1 :contents-begin 2218 :contents-end 2817 :robust-begin 2220 :robust-end 2815 :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 2194 :title (#("Pushing to DockerHub" 0 20 (:parent #53))) :mode nil :granularity nil :parent #46) (section (:begin 2218 :end 2817 :contents-begin 2218 :contents-end 2817 :robust-begin 2218 :robust-end 2815 :post-blank 0 :post-affiliated 2218 :mode section :granularity nil :parent #53) (paragraph (:begin 2218 :end 2325 :contents-begin 2218 :contents-end 2324 :post-blank 1 :post-affiliated 2218 :mode planning :granularity nil :parent #56) #("We use DockerHub to store the docker images from which we use on our\nCI environment using Github Actions.\n" 0 106 (:parent #59))) (paragraph (:begin 2325 :end 2447 :contents-begin 2325 :contents-end 2446 :post-blank 1 :post-affiliated 2325 :mode nil :granularity nil :parent #56) #("To push to dockerhub, first get the image name by running " 0 58 (:parent #60)) (verbatim (:begin 2383 :end 2398 :post-blank 0 :value "docker\nimages" :parent #60)) #(". Push to dockerhub using a command similar to:\n" 0 48 (:parent #60))) (fixed-width (:begin 2447 :end 2494 :value "docker push bonfacekilz/genenetwork2:latest" :post-blank 2 :post-affiliated 2447 :mode nil :granularity nil :parent #56)) (paragraph (:begin 2494 :end 2537 :contents-begin 2494 :contents-end 2536 :post-blank 1 :post-affiliated 2494 :mode nil :granularity nil :parent #56) #("Right now, we have 2 images on DockerHub:\n" 0 42 (:parent #62))) (plain-list (:type unordered :begin 2537 :end 2817 :contents-begin 2537 :contents-end 2817 :structure ((2537 0 "- " nil nil nil 2701) (2701 0 "- " nil nil nil 2817)) :post-blank 0 :post-affiliated 2537 :mode nil :granularity nil :parent #56) (item (:bullet "- " :begin 2537 :end 2701 :contents-begin 2539 :contents-end 2701 :checkbox nil :counter nil :structure ((2537 0 "- " nil nil nil 2701) (2701 0 "- " nil nil nil 2817)) :pre-blank 0 :post-blank 0 :post-affiliated 2537 :tag nil :mode item :granularity nil :parent #63) (paragraph (:begin 2539 :end 2701 :contents-begin 2539 :contents-end 2701 :post-blank 0 :post-affiliated 2539 :mode nil :granularity nil :parent #66) (link (:type "https" :path "//hub.docker.com/repository/docker/bonfacekilz/python2-genenetwork2" :format plain :raw-link "https://hub.docker.com/repository/docker/bonfacekilz/python2-genenetwork2" :application nil :search-option nil :begin 2539 :end 2612 :contents-begin nil :contents-end nil :post-blank 0 :parent #69)) #(":\n Contains the python2 version of gn2. 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:post-affiliated 276 :mode section :granularity nil :parent #343) (paragraph (:begin 276 :end 600 :contents-begin 276 :contents-end 599 :post-blank 1 :post-affiliated 276 :mode planning :granularity nil :parent #346) #("The CI(Continuous Integration) system for Genenetwork2 uses " 0 60 (:parent #349)) (link (:type "https" :path "//github.com/features/actions" :format bracket :raw-link "https://github.com/features/actions" :application nil :search-option nil :begin 336 :end 391 :contents-begin 375 :contents-end 389 :post-blank 0 :parent #349) #("Github\nActions" 0 14 (:parent #353))) #(". As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #349))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #346) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #350)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #350) #("here" 0 4 (:parent #354))) #(". This\ndocument will not get into that. 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As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #57))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #54) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #58)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #58) #("here" 0 4 (:parent #62))) #(". This\ndocument will not get into that. 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As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #9))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #6) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #10)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #10) #("here" 0 4 (:parent #14))) #(". This\ndocument will not get into that. It's assumed that you have a working\ndocker setup.\n" 0 91 (:parent #10))) (paragraph (:begin 830 :end 925 :contents-begin 830 :contents-end 925 :post-blank 0 :post-affiliated 830 :mode nil :granularity nil :parent #6) #("The rest of this document outlines how the docker container used in\nthe CI builds was created.\n" 0 95 (:parent #11))))) (headline (:raw-value "Creating the Docker Images" :begin 926 :end 2194 :pre-blank 1 :contents-begin 956 :contents-end 2193 :robust-begin 958 :robust-end 2191 :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 926 :title (#("Creating the Docker Images" 0 26 (:parent #4))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 2817 :end 2817 :robust-begin 3 :robust-end 2815 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 956 :end 2194 :contents-begin 956 :contents-end 2193 :robust-begin 956 :robust-end 2191 :post-blank 1 :post-affiliated 956 :mode section :granularity nil :parent #4) (paragraph (:begin 956 :end 1071 :contents-begin 956 :contents-end 1070 :post-blank 1 :post-affiliated 956 :mode planning :granularity nil :parent #7) #("The general idea is that GUIX is used to generate a set of binaries,\nwhich will be added to a base mariaDB image.\n" 0 114 (:parent #10))) (paragraph (:begin 1071 :end 1117 :contents-begin 1071 :contents-end 1116 :post-blank 1 :post-affiliated 1071 :mode nil :granularity nil :parent #7) #("First create the gn2 tar archive by running:\n" 0 45 (:parent #11))) (src-block (:language "sh" :switches nil :parameters nil :begin 1117 :end 1343 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "env GUIX_PACKAGE_PATH=\"/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules\" \\\n ./pre-inst-env guix pack --no-grafts\\\n -S /gn2-profile=/ \\\n screen genenetwork2\n" :post-blank 1 :post-affiliated 1117 :mode nil :granularity nil :parent #7)) (paragraph (:begin 1343 :end 1387 :contents-begin 1343 :contents-end 1386 :post-blank 1 :post-affiliated 1343 :mode nil :granularity nil :parent #7) #("The output will look something similar to:\n" 0 43 (:parent #13))) (fixed-width (:begin 1387 :end 1454 :value "/gnu/store/x3m77vwaqcwba24p5s4lrb7w2ii16lj9-tarball-pack.tar.gz" :post-blank 2 :post-affiliated 1387 :mode nil :granularity nil :parent #7)) (paragraph (:begin 1454 :end 1640 :contents-begin 1454 :contents-end 1639 :post-blank 1 :post-affiliated 1454 :mode nil :granularity nil :parent #7) #("Now create a folder from which will host the following dockerfile. 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Note that mariadb is the base image\nsince it already has mariadb installed for us.\n" 0 185 (:parent #15))) (src-block (:language "conf" :switches nil :parameters nil :begin 1640 :end 1847 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "FROM mariadb:latest\n\nCOPY ./gn2.tar.gz /tmp/gn2.tar.gz\nRUN tar -xzf /tmp/gn2.tar.gz -C / && rm -f /tmp/gn2.tar.gz && \\\n mkdir -p /usr/local/mysql /genotype_files/genotype/json\n" :post-blank 1 :post-affiliated 1640 :mode nil :granularity nil :parent #7)) (paragraph (:begin 1847 :end 1895 :contents-begin 1847 :contents-end 1894 :post-blank 1 :post-affiliated 1847 :mode nil :granularity nil :parent #7) #("Build the image(Note the fullstop at the end):\n" 0 47 (:parent #17))) (fixed-width (:begin 1895 :end 1955 :value "sudo docker build -t genenetwork2:latest -f Dockerfile ." :post-blank 2 :post-affiliated 1895 :mode nil :granularity nil :parent #7)) (paragraph (:begin 1955 :end 2009 :contents-begin 1955 :contents-end 2008 :post-blank 1 :post-affiliated 1955 :mode nil :granularity nil :parent #7) #("To load the image interactively you've just created:\n" 0 53 (:parent #19))) (fixed-width (:begin 2009 :end 2054 :value "docker run -ti \"genenetwork2:latest\" bash" :post-blank 2 :post-affiliated 2009 :mode nil :granularity nil :parent #7)) (paragraph (:begin 2054 :end 2141 :contents-begin 2054 :contents-end 2140 :post-blank 1 :post-affiliated 2054 :mode nil :granularity nil :parent #7) #("Assuming you have a docker instance running, you could always run\ncommands in it e.g:\n" 0 86 (:parent #21))) (fixed-width (:begin 2141 :end 2193 :value "docker run \"genenetwork2:latest\" python --version" :post-blank 1 :post-affiliated 2141 :mode nil :granularity nil :parent #7)))) (headline (:raw-value "Pushing to DockerHub" :begin 2194 :end 2817 :pre-blank 1 :contents-begin 2218 :contents-end 2817 :robust-begin 2220 :robust-end 2815 :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 2194 :title (#("Pushing to DockerHub" 0 20 (:parent #5))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 2817 :end 2817 :robust-begin 3 :robust-end 2815 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 2218 :end 2817 :contents-begin 2218 :contents-end 2817 :robust-begin 2218 :robust-end 2815 :post-blank 0 :post-affiliated 2218 :mode section :granularity nil :parent #5) (paragraph (:begin 2218 :end 2325 :contents-begin 2218 :contents-end 2324 :post-blank 1 :post-affiliated 2218 :mode planning :granularity nil :parent #8) #("We use DockerHub to store the docker images from which we use on our\nCI environment using Github Actions.\n" 0 106 (:parent #11))) (paragraph (:begin 2325 :end 2447 :contents-begin 2325 :contents-end 2446 :post-blank 1 :post-affiliated 2325 :mode nil :granularity nil :parent #8) #("To push to dockerhub, first get the image name by running " 0 58 (:parent #12)) (verbatim (:begin 2383 :end 2398 :post-blank 0 :value "docker\nimages" :parent #12)) #(". 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As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #11))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #8) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #12)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #12) #("here" 0 4 (:parent #16))) #(". This\ndocument will not get into that. It's assumed that you have a working\ndocker setup.\n" 0 91 (:parent #12))) (paragraph (:begin 830 :end 925 :contents-begin 830 :contents-end 925 :post-blank 0 :post-affiliated 830 :mode nil :granularity nil :parent #8) #("The rest of this document outlines how the docker container used in\nthe CI builds was created.\n" 0 95 (:parent #13))))) (headline (:raw-value "Creating the Docker Images" :begin 926 :end 2194 :pre-blank 1 :contents-begin 956 :contents-end 2193 :robust-begin 958 :robust-end 2191 :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 926 :title (#("Creating the Docker Images" 0 26 (:parent #6))) :mode nil :granularity nil :parent #0) (section (:begin 956 :end 2194 :contents-begin 956 :contents-end 2193 :robust-begin 956 :robust-end 2191 :post-blank 1 :post-affiliated 956 :mode section :granularity nil :parent #6) (paragraph (:begin 956 :end 1071 :contents-begin 956 :contents-end 1070 :post-blank 1 :post-affiliated 956 :mode planning :granularity nil :parent #9) #("The general idea is that GUIX is used to generate a set of binaries,\nwhich will be added to a base mariaDB image.\n" 0 114 (:parent #12))) (paragraph (:begin 1071 :end 1117 :contents-begin 1071 :contents-end 1116 :post-blank 1 :post-affiliated 1071 :mode nil :granularity nil :parent #9) #("First create the gn2 tar archive by running:\n" 0 45 (:parent #13))) (src-block (:language "sh" :switches nil :parameters nil :begin 1117 :end 1343 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "env GUIX_PACKAGE_PATH=\"/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules\" \\\n ./pre-inst-env guix pack --no-grafts\\\n -S /gn2-profile=/ \\\n screen genenetwork2\n" :post-blank 1 :post-affiliated 1117 :mode nil :granularity nil :parent #9)) (paragraph (:begin 1343 :end 1387 :contents-begin 1343 :contents-end 1386 :post-blank 1 :post-affiliated 1343 :mode nil :granularity nil :parent #9) #("The output will look something similar to:\n" 0 43 (:parent #15))) (fixed-width (:begin 1387 :end 1454 :value "/gnu/store/x3m77vwaqcwba24p5s4lrb7w2ii16lj9-tarball-pack.tar.gz" :post-blank 2 :post-affiliated 1387 :mode nil :granularity nil :parent #9)) (paragraph (:begin 1454 :end 1640 :contents-begin 1454 :contents-end 1639 :post-blank 1 :post-affiliated 1454 :mode nil :granularity nil :parent #9) #("Now create a folder from which will host the following dockerfile. 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:post-affiliated 276 :mode section :granularity nil :parent #343) (paragraph (:begin 276 :end 600 :contents-begin 276 :contents-end 599 :post-blank 1 :post-affiliated 276 :mode planning :granularity nil :parent #346) #("The CI(Continuous Integration) system for Genenetwork2 uses " 0 60 (:parent #349)) (link (:type "https" :path "//github.com/features/actions" :format bracket :raw-link "https://github.com/features/actions" :application nil :search-option nil :begin 336 :end 391 :contents-begin 375 :contents-end 389 :post-blank 0 :parent #349) #("Github\nActions" 0 14 (:parent #353))) #(". As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #349))) (paragraph (:begin 600 :end 830 :contents-begin 600 :contents-end 829 :post-blank 1 :post-affiliated 600 :mode nil :granularity nil :parent #346) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #350)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil :begin 654 :end 738 :contents-begin 732 :contents-end 736 :post-blank 0 :parent #350) #("here" 0 4 (:parent #354))) #(". This\ndocument will not get into that. 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