diff options
Diffstat (limited to 'gn/packages/genenetwork.scm')
| -rw-r--r-- | gn/packages/genenetwork.scm | 664 |
1 files changed, 356 insertions, 308 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 36d3ae6..10619da 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -5,6 +5,7 @@ #:use-module (guix packages) #:use-module (guix utils) #:use-module (guix download) + #:use-module (guix git) #:use-module (guix git-download) #:use-module (guix build-system cargo) #:use-module (guix build-system gnu) @@ -14,6 +15,7 @@ #:use-module (guix scripts graph) #:use-module (guix store) #:use-module (guix gexp) + #:use-module (guix packages) #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages bioconductor) @@ -110,10 +112,11 @@ ((#:tests? _ #f) #f))))) (define-public genenetwork3 - (let ((commit "f52247c15f3694f3dd5fd0fd79c3e15376137e07")) + (let ((commit "6bb4a5f05c1a2c96b7da1780ae4a1d70c7cc4afb") + (revision "5")) (package (name "genenetwork3") - (version (git-version "0.1.0" "3" commit)) + (version (git-version "0.1.0" revision commit)) (source (origin (method git-fetch) @@ -123,52 +126,51 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0ac0dr8dny65x4xvm8gw6ap3g8g0j933ipy9116idcws31rk2adk")))) + "13nvi2gwwb0shra0d9rsfhppa9ky4bhgh1zgb34790ax0g9lwa97")))) (inputs (list python-click)) (native-inputs (list python-hypothesis python-mypy python-mypy-extensions - python-pylint - python-pytest - python-pytest-mock)) + python-pylint)) (propagated-inputs - (list gemma-wrapper - python-wrapper - csvdiff + (list csvdiff + diffutils + gemma-wrapper gn-rust-correlation - python-bcrypt ;; Replace use of bcrypt with argon below - python-argon2-cffi + python-argon2-cffi + python-authlib + python-bcrypt ;; Replace use of bcrypt with argon + python-biopython + python-email-validator python-flask python-flask-cors - ;; Not working in Python > 3.8 - ;; python-ipfshttpclient python-lmdb python-mysqlclient python-numpy python-pandas - ;; python-pingouin << build failing python-pingouin-without-tests python-plotly - python-scikit-learn + python-pyld python-pymonad + python-pytest + python-pytest-mock python-redis python-requests + python-scikit-learn python-scipy - python-authlib python-sparqlwrapper - python-email-validator + python-wrapper python-xapian-bindings + r + r-ctl r-optparse r-qtl r-rjson r-stringi r-wgcna - r-ctl - rust-qtlreaper - diffutils - yoyo-migrations)) + rust-qtlreaper)) (build-system python-build-system) (arguments (list #:phases @@ -183,10 +185,11 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "bfe557dc1e537dc78a82a30817ecf2ca3004d978")) + (let ((commit "b9e04ad79e0039edba25d58f8bc03e4d2a17583b") + (revision "4")) (package (name "genenetwork2") - (version (git-version "3.11" "2" commit)) + (version (git-version "3.11" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -195,273 +198,318 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "1bn0j0fpk4hcicgfird62x5wq2n6lj4rs1ggw69dcxyf4qdxbk5d")))) + "1ri56g5hl2n0q7cz15sbvjmrr5pmsrp274frkvvcgr9ddxjlzd9p")))) (native-inputs (list graphviz)) (propagated-inputs - `(("genenetwork3" ,genenetwork3) - ("parallel" ,parallel) ;; GNU parallel - ("coreutils" ,coreutils) - ("git" ,git) - ("which" ,which) - ("grep" ,grep) - ("r" ,r) - ("r-ctl" ,r-ctl) - ("r-qtl" ,r-qtl) - ("r-wgcna" ,r-wgcna) - ("redis" ,redis) - ("mariadb" ,mariadb) - ("gemma" ,gemma-gn2) - ("gemma-wrapper" ,gemma-wrapper) - ("plink-ng-gn" ,plink-ng-gn) - ("rust-qtlreaper" ,rust-qtlreaper) - ("gn-rust-correlation" ,gn-rust-correlation) - ("glibc-utf8-locales" ,glibc-utf8-locales) - ("nginx" ,nginx) - ("python" ,python-wrapper) - ("python-pillow" ,python-pillow) - ("python-coverage" ,python-coverage) - ("python-configparser" ,python-configparser) ;; maintenance/scripts - ("python-flask" ,python-flask) - ("gunicorn" ,gunicorn) - ("python-autopep8" ,python-autopep8) - ("python-cssselect" ,python-cssselect) - ("python-flask-debugtoolbar" ,python-flask-debugtoolbar) - ("python-htmlgen" ,python-htmlgen) - ("python-ijson" ,python-ijson) - ("python-jinja2" ,python-jinja2) - ("python-pytest" ,python-pytest) - ("python-pytest-mock" ,python-pytest-mock) - ("python-sqlalchemy" ,python-sqlalchemy) - ("python-setuptools" ,python-setuptools) - ("python-scipy" ,python-scipy) - ("python-lxml" ,python-lxml) - ("python-mysqlclient" ,python-mysqlclient) - ("python-mypy" ,python-mypy) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-pylint" ,python-pylint) - ("python-pymonad" ,python-pymonad) - ("python-redis" ,python-redis) - ("python-requests" ,python-requests) - ("python-simplejson" ,python-simplejson) - ("python-markdown" ,python-markdown) - ("python-rdflib" ,python-rdflib) - ("python-authlib" ,python-authlib) - ("python-flask-session" ,python-flask-session) - ;; TODO: Get rid of Python R bindings - ("python-rpy2" ,python-rpy2) - ("python-beautifulsoup4" ,python-beautifulsoup4) - ;; Disable for now. Build fails on Penguin2 - ;; ("python-flask-socketio" ,python-flask-socketio) - ("python-xlsxwriter" ,python-xlsxwriter) - ;; All the external js dependencies - ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher) - ("javascript-cytoscape" ,javascript-cytoscape) - ("javascript-panzoom" ,javascript-cytoscape-panzoom) - ("javascript-qtip" ,javascript-cytoscape-qtip) - ("javascript-chroma" ,javascript-chroma) - ("javascript-d3-tip" ,javascript-d3-tip) - ("javascript-jscolor" ,javascript-jscolor) - ("javascript-colorbox" ,javascript-colorbox) - ("javascript-jszip" ,javascript-jszip) - ("js-jstat" ,js-jstat) - ("js-md5" ,js-md5) - ("js-parsley" ,js-parsley) - ("javascript-plotly" ,javascript-plotly) - ("javascript-typeahead" ,javascript-typeahead) - ("js-underscore" ,js-underscore) - ("js-smart-time-ago" ,js-smart-time-ago) - ("javascript-nouislider" ,javascript-nouislider) - ("javascript-purescript-genome-browser" ,javascript-purescript-genome-browser) - ("javascript-ckeditor" ,javascript-ckeditor) - ("javascript-datatables" ,javascript-datatables) - ("javascript-datatables-scroller" ,javascript-datatables-scroller) - ("javascript-datatables-buttons" ,javascript-datatables-buttons) - ("javascript-datatables-buttons-bootstrap" ,javascript-datatables-buttons-bootstrap) - ("javascript-datatables-plugins" ,javascript-datatables-plugins) - ("javascript-datatables-col-reorder" ,javascript-datatables-col-reorder) - ("javascript-datatables-col-resize" ,javascript-datatables-col-resize) - ("javascript-datatables-buttons-styles" ,javascript-datatables-buttons-styles) - ("javascript-shapiro-wilk" ,javascript-shapiro-wilk) - ("javascript-underscore-string" ,javascript-underscore-string) - ("javascript-qtip2" ,javascript-qtip2) - ("javascript-d3js" ,javascript-d3js) - ("javascript-nvd3" ,javascript-nvd3) - ("javascript-bootstrap" ,javascript-bootstrap) - ("javascript-jquery" ,javascript-jquery) - ("javascript-zxcvbn" ,javascript-zxcvbn) - ("javascript-jquery-ui" ,javascript-jquery-ui) - ("javascript-jquery-cookie" ,javascript-jquery-cookie) - ("javascript-xterm" ,javascript-xterm) - ("javascript-xterm-style" ,javascript-xterm-style) - ("javascript-xterm-addon-fit",javascript-xterm-addon-fit) - ("javascript-font-awesome" ,javascript-font-awesome))) + (list genenetwork3 + coreutils + gemma + gemma-wrapper + git + glibc-utf8-locales + gn-rust-correlation + grep + gunicorn + javascript-bootstrap + javascript-chroma + javascript-ckeditor + javascript-colorbox + javascript-cytoscape + javascript-cytoscape-panzoom + javascript-cytoscape-qtip + javascript-d3-tip + javascript-d3js ;; very old + javascript-d3js-7 + javascript-d3panels + javascript-datatables + javascript-datatables-buttons + javascript-datatables-buttons-bootstrap + javascript-datatables-buttons-styles + javascript-datatables-col-reorder + javascript-datatables-col-resize + javascript-datatables-plugins + javascript-datatables-scroller + javascript-font-awesome + javascript-htmx + javascript-jquery + javascript-jquery-cookie + javascript-jquery-ui + javascript-jscolor + javascript-jszip + javascript-linkify + javascript-linkify-html + javascript-nouislider + javascript-nvd3 + javascript-plotly + javascript-purescript-genome-browser + javascript-qtip2 + javascript-shapiro-wilk + javascript-twitter-post-fetcher + javascript-typeahead + javascript-uikit + javascript-underscore-string + javascript-zxcvbn + js-jstat + js-md5 + js-parsley + js-smart-time-ago + js-underscore + mariadb + nginx + parallel + plink-ng-gn + python-authlib + python-autopep8 + python-beautifulsoup4 + python-configparser + python-coverage + python-cssselect + python-flask + python-flask-debugtoolbar + python-flask-session + python-htmlgen + python-ijson + python-jinja2 + python-lxml + python-markdown + python-mypy + python-mysqlclient + python-numpy + python-pandas + python-pillow + python-pylint + python-pymonad + python-pytest + python-pytest-mock + python-rdflib + python-redis + python-requests + python-rpy2 + python-scipy + python-setuptools + python-simplejson + python-sqlalchemy + python-wrapper + python-xlsxwriter + r + r-ctl + r-qtl + r-wgcna + redis + rust-qtlreaper + which + ; javascript-xterm -- disabled until we know what to do with it, not working on production + ; javascript-xterm-style + ; javascript-xterm-addon-fit + )) (inputs - `(("javascript-colorbox" ,(package-source javascript-colorbox)))) + (list javascript-colorbox)) (build-system python-build-system) (arguments - `(#:tests? #f ; no 'setup.py test' + (list #:tests? #f + #:phases + #~(modify-phases %standard-phases + (delete 'reset-gzip-timestamps) + (add-after 'unpack 'fix-paths-to-static-files + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Set absolute store paths to installed static files. + (substitute* "gn2/wqflask/marker_regression/display_mapping_results.py" + (("\\./gn2/wqflask/static/fonts") + (string-append (site-packages inputs outputs) + "/gn2/wqflask/static/fonts"))) + (substitute* "gn2/wqflask/views.py" + (("\\./gn2/wqflask/static/gif/error") + (string-append (site-packages inputs outputs) + "/gn2/wqflask/static/gif/error"))) + (substitute* "gn2/wqflask/app_errors.py" + (("\\./gn2/wqflask/static/gif/error") + (string-append (site-packages inputs outputs) + "/gn2/wqflask/static/gif/error"))))) + (add-after 'unpack 'fix-paths-scripts + (lambda _ + (substitute* "bin/genenetwork2" + (("/usr/bin/env") (which "env")) + (("python ") (string-append (which "python3") " ")) + (("readlink") (which "readlink")) + (("dirname") (which "dirname")) + (("basename") (which "basename")) + (("cat") (which "cat")) + (("echo") (which "echo")) + (("redis-server") (which "redis-server")) + (("git") (which "git")) + (("grep") (which "grep")) + (("rm") (which "rm")) + (("which") (which "which"))))) + (add-before 'install 'fix-paths + (lambda* (#:key inputs #:allow-other-keys) + (let* ((plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) + (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))) + (substitute* '("gn2/default_settings.py") + (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) + (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" ))))))))) + (home-page "http://genenetwork.org/") + (synopsis "Full genenetwork services") + (description "Genenetwork installation sumo.") + (license license:agpl3+)))) + +(define-public genenetwork3-stable + (let ((commit "e5569c3bb1c0d59ff7142273c5f51fe19f06cfe8") + (revision "1")) + (package + (inherit genenetwork3) + (name "genenetwork3-stable") + (version (string-append (git-version "3.11" revision commit))) + (arguments + (list + #:tests? #f #:phases - (modify-phases %standard-phases - (delete 'reset-gzip-timestamps) - (add-after 'unpack 'fix-paths-scripts - (lambda _ - (substitute* "bin/genenetwork2" - (("/usr/bin/env") (which "env")) - (("python ") (string-append (which "python3") " ")) - (("readlink") (which "readlink")) - (("dirname") (which "dirname")) - (("basename") (which "basename")) - (("cat") (which "cat")) - (("echo") (which "echo")) - (("redis-server") (which "redis-server")) - (("git") (which "git")) - (("grep") (which "grep")) - (("rm") (which "rm")) - (("which") (which "which"))) - #t)) - ; (add-after 'unpack 'patch-javascript - ; (lambda* (#:key inputs #:allow-other-keys) - ; (let ((colorbox (assoc-ref inputs "javascript-colorbox")) - ; (gn2 "/share/genenetwork2/javascript/")) - ; (delete-file-recursively "wqflask/wqflask/static/packages/colorbox") - ; (copy-recursively colorbox "wqflask/wqflask/static/packages/colorbox") - ; #t))) - (add-before 'install 'fix-paths - (lambda* (#:key inputs #:allow-other-keys) - (let* ( - ; (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2")) - ; (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) - (plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) - (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) - ) + #~(modify-phases %standard-phases + (add-before 'build 'update-paths + (lambda _ + (for-each (lambda (fn) + (substitute* (string-append "gn3/" fn) + (("scripts/") + (string-append #$output "/scripts/")))) + '("api/rqtl.py" + "computations/wgcna.py" + "computations/ctl.py" + "api/general.py")))) + (add-before 'install 'install-scripts + (lambda _ + (begin + (mkdir (string-append #$output "scripts")) + (for-each (lambda (fn) + (install-file fn + (string-append #$output "/scripts"))) + '("scripts/rqtl_wrapper.R" + "scripts/ctl_analysis.R" + "scripts/wgcna_analysis.R" + )))))))) - (substitute* '("etc/default_settings.py") - ; (("^GENENETWORK_FILES +=.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) - ; (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) - (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) - (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )) - ) - ))) - ; (add-after 'install 'generate-graph - ; (lambda* (#:key inputs outputs #:allow-other-keys) - ; (call-with-output-file - ; (string-append - ; (assoc-ref outputs "out") - ; "/lib/python" - ; (python-version (assoc-ref inputs "python")) - ; "/site-packages" - ; "/wqflask/dependency-graph.html") - ; (lambda (port) - ; (format - ; port "~a" - ; ,(call-with-output-string - ; (lambda (p) - ; (with-output-to-port p - ; (lambda () - ; (run-with-store - ; (open-connection) - ; (export-graph - ; (list this-package) - ; p - ; #:node-type %package-node-type - ; #:backend %d3js-backend))))))))))) - ;(add-after 'install 'generate-dag-svg-file - ; (lambda* (#:key inputs outputs #:allow-other-keys) - ; (let* ((output-dir - ; (string-append - ; (assoc-ref outputs "out") - ; "/lib/python" - ; (python-version (assoc-ref inputs "python")) - ; "/site-packages/wqflask/")) - ; (dot-file - ; (string-append - ; output-dir - ; "dependency-graph.dot")) - ; (svg-file - ; (string-append - ; output-dir - ; "dependency-graph.svg"))) - ; (begin - ; (call-with-output-file - ; dot-file - ; (lambda (port) - ; (format - ; port "~a" - ; ,(call-with-output-string - ; (lambda (p) - ; (with-output-to-port p - ; (lambda () - ; (run-with-store - ; (open-connection) - ; (export-graph - ; (list this-package) - ; p - ; #:node-type %package-node-type - ; #:backend %graphviz-backend))))))))) - ; (invoke "dot" "-Tsvg" "-o" svg-file dot-file))))) + (source + (git-checkout + (url "https://github.com/genenetwork/genenetwork3") + (branch "prod")))))) - ;; TODO: Use this to replace the two previous phases. - ;(add-after 'install 'install-generated-files - ; (lambda* (#:key inputs outputs #:allow-other-keys) - ; (let ((output-dir - ; (string-append - ; (assoc-ref outputs "out") - ; "/lib/python" - ; (python-version (assoc-ref inputs "python")) - ; "/site-packages/wqflask/"))) - ; (install-file (string-append %dag-svg-file "/dependency-graph.dot") output-dir) - ; (install-file (string-append %dag-svg-file "/dependency-graph.svg") output-dir) - ; (install-file (string-append %genenetwork-graph "/dependency-graph.html") output-dir) - ; #t))) +(define-public genenetwork2-stable + (let ((commit "95e634ca90d52922812b93df162686b348288651") + (revision "1")) + (package + (inherit genenetwork2) + (name "genenetwork2-stable") + (version (string-append "stable-" (git-version "3.12" revision commit))) + (source + (git-checkout + (url "https://github.com/genenetwork/genenetwork2") + (branch "prod"))) + (arguments + (list + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'update-font-paths + (lambda* (#:key inputs outputs #:allow-other-keys) + (for-each (lambda (fn) + (substitute* (string-append "gn2/" fn) + (("\\./gn2/wqflask/static/fonts/") + (string-append (site-packages inputs outputs) "/gn2/wqflask/static/fonts/")))) + '("utility/Plot.py" + "wqflask/marker_regression/display_mapping_results.py")))) + )))))) - #! - (add-after 'install 'generate-dependency-file - (lambda* (#:key inputs outputs #:allow-other-keys) - (call-with-output-file - (string-append - (assoc-ref outputs "out") - "/lib/python" - (python-version (assoc-ref inputs "python")) - "/site-packages" - "/wqflask/DEPENDENCIES.md" - ) - (lambda (port) - (format - port " -#### System Inputs (generated from ~a package defined in ~a) -|Name | Description | -|-----|-------------| -~a -" - ,(package-name this-package) - (string-append - "[genenetwork.scm]" - "(http://git.genenetwork.org/" - "guix-bioinformatics/guix-bioinformatics" - "/src/branch/master/gn/packages/" - "genenetwork.scm)") - ,(apply - string-append - (map - (lambda (input) - (let* ((pkg (cadr input)) - (name (package-name pkg)) - (version (package-version pkg)) - (home-page (package-home-page pkg)) - (description (package-synopsis pkg))) - (string-append - "| **[" name "](" home-page ")** v" - version"| " - description " |\n"))) - (package-propagated-inputs this-package)))))))) - !# - ))) - (home-page "http://genenetwork.org/") - (synopsis "Full genenetwork services") - (description "Genenetwork installation sumo.") - (license license:agpl3+)))) +(define-public gn-uploader + (let ((commit "60fde66e02dba842b20fa126ff3b2ed9ec2638e6") + (version "0.0.1")) + (package + (name "gn-uploader") + (version (string-append version "-" (string-take commit 8))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://git.genenetwork.org/gn-uploader") + (commit commit))) + (hash + (content-hash + (base32 + "1q04viyf7d0q30k3424hrzsh9wxhhgs7hywlhzl3m68jki4zq1i7"))))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-m" "unit_test"))))))) + (native-inputs + (list python-mypy + python-pylint + python-pytest + python-hypothesis)) + (propagated-inputs + (list gunicorn + python-redis + python-flask + python-pyyaml + python-jsonpickle + python-mysqlclient + javascript-jquery + javascript-bootstrap)) + (synopsis "GeneNetwork Quality Control Application") + (description + "gn-uploader is a service allowing upload of new data into GeneNetwork, + that does quality control for the data files that is being uploaded to ensure + it fulfils all conditions before it can be accepted.") + (home-page "https://git.genenetwork.org/gn-uploader") + (license license:agpl3+)))) + +(define-public gn-auth + (package + (name "gn-auth") + (version "1.0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/genenetwork/gn-auth.git") + (commit "cd6eebd85d32feb289ccecd1aee45fb40b03d77f"))) + (hash + (content-hash + (base32 + "06slj3z110mbc46qncdvyi29y85zkqxl76n89dxjp5wjfqxw0nsl"))))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-k" "unit_test"))))))) + (native-inputs + (list python-hypothesis + python-mypy + python-mypy-extensions + python-pylint + python-pytest + python-pytest-mock)) + (propagated-inputs + (list gunicorn + python-argon2-cffi + python-authlib + python-email-validator + python-flask + python-flask-cors + python-mysqlclient + python-pymonad + python-redis + yoyo-migrations)) + (home-page "https://github.com/genenetwork/gn-auth") + (synopsis "Authentication and Authorisation server for GeneNetwork services") + (description "Authentication and Authorisation server for GeneNetwork services.") + (license license:agpl3+))) ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x @@ -469,41 +517,41 @@ (define-public genenetwork2-files-small (let ((pfff "xx")) (package - (name "genenetwork2-files-small") - (version "1.0") - (source - (origin - (method url-fetch) - (uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4") - (file-name (string-append name "-" pfff)) - (sha256 - (base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj")))) - (build-system trivial-build-system) - (native-inputs `(("lz4" ,lz4) - ("tar" ,tar) - ("source" ,source))) + (name "genenetwork2-files-small") + (version "1.0") + (source + (origin + (method url-fetch) + (uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4") + (file-name (string-append name "-" pfff)) + (sha256 + (base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj")))) + (build-system trivial-build-system) + (native-inputs `(("lz4" ,lz4) + ("tar" ,tar) + ("source" ,source))) - (arguments - `(#:modules ((guix build utils)) - #:builder - (let* ((out (assoc-ref %outputs "out")) - (name "gn2_data_s") - (tarfn (string-append name ".tar")) - (targetdir (string-append out "/share/genenetwork2/"))) + (arguments + `(#:modules ((guix build utils)) + #:builder + (let* ((out (assoc-ref %outputs "out")) + (name "gn2_data_s") + (tarfn (string-append name ".tar")) + (targetdir (string-append out "/share/genenetwork2/"))) (begin (use-modules (guix build utils)) (let ((source (assoc-ref %build-inputs "source")) (lz4unpack (string-append (assoc-ref %build-inputs "lz4") "/bin/lz4")) (tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar"))) (and - (zero? (system* lz4unpack source "-d" tarfn)) - (zero? (system* tar "xf" tarfn)) - (mkdir-p targetdir) - (copy-recursively name targetdir))))))) - (home-page "http://genenetwork.org/") - (synopsis "Small file archive to run on genenetwork") - (description "Genenetwork genotype and mapping files.") - (license license:agpl3+)))) + (zero? (system* lz4unpack source "-d" tarfn)) + (zero? (system* tar "xf" tarfn)) + (mkdir-p targetdir) + (copy-recursively name targetdir))))))) + (home-page "http://genenetwork.org/") + (synopsis "Small file archive to run on genenetwork") + (description "Genenetwork genotype and mapping files.") + (license license:agpl3+)))) (define-public genenetwork2-database-small (let ((md5 "93e745e9c")) |