diff options
Diffstat (limited to 'gn/packages/genenetwork.scm')
| -rw-r--r-- | gn/packages/genenetwork.scm | 387 |
1 files changed, 126 insertions, 261 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 890d7e5..6be016e 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -202,270 +202,135 @@ (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-htmx" ,javascript-htmx) - ("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 + parallel + coreutils + git + which + grep + r + r-ctl + r-qtl + r-wgcna + redis + mariadb + gemma + gemma-wrapper + plink-ng-gn + rust-qtlreaper + gn-rust-correlation + glibc-utf8-locales + nginx + python-wrapper + python-pillow + python-coverage + python-configparser + python-flask + gunicorn + python-autopep8 + python-cssselect + python-flask-debugtoolbar + python-htmlgen + python-ijson + python-jinja2 + python-pytest + python-pytest-mock + python-sqlalchemy + python-setuptools + python-scipy + python-lxml + python-mysqlclient + python-mypy + python-numpy + python-pandas + python-pylint + python-pymonad + python-redis + python-requests + python-simplejson + python-markdown + python-rdflib + python-authlib + python-flask-session + python-rpy2 + python-beautifulsoup4 + python-xlsxwriter + javascript-twitter-post-fetcher + javascript-cytoscape + javascript-cytoscape-panzoom + javascript-cytoscape-qtip + javascript-chroma + javascript-d3-tip + javascript-jscolor + javascript-colorbox + javascript-jszip + js-jstat + js-md5 + js-parsley + javascript-plotly + javascript-typeahead + js-underscore + js-smart-time-ago + javascript-nouislider + javascript-purescript-genome-browser + javascript-ckeditor + javascript-datatables + javascript-datatables-scroller + javascript-datatables-buttons + javascript-datatables-buttons-bootstrap + javascript-datatables-plugins + javascript-datatables-col-reorder + javascript-datatables-col-resize + javascript-datatables-buttons-styles + javascript-shapiro-wilk + javascript-underscore-string + javascript-htmx + javascript-qtip2 + javascript-d3js + javascript-nvd3 + javascript-bootstrap + javascript-jquery + javascript-zxcvbn + javascript-jquery-ui + javascript-jquery-cookie + javascript-xterm + javascript-xterm-style + javascript-xterm-addon-fit + javascript-font-awesome)) (inputs - `(("javascript-colorbox" ,(package-source javascript-colorbox)))) + (list javascript-colorbox)) (build-system python-build-system) (arguments - `(#:tests? #f ; no 'setup.py test' - #: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")) - ) - - (substitute* '("gn2/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))))) - - ;; 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))) - - #! - (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+)))) + (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"))))) + (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 gnqc-py (package |