diff options
| -rw-r--r-- | gn/packages/genenetwork.scm | 387 |
1 files changed, 232 insertions, 155 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 4c3ef26..60173a9 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -293,7 +293,6 @@ Graphical Fragment Assembly} files and related formats.") (define-public genenetwork2 (let ((commit "84cbf35adbb15c79638372d108308edb05f12683")) (package - (inherit python2-genenetwork2) (name "genenetwork2") (version (string-append "3.11-guix-" (string-take commit 7) )) (source (origin @@ -308,166 +307,244 @@ Graphical Fragment Assembly} files and related formats.") (native-inputs `(("graphviz" ,graphviz))) (propagated-inputs - (let ((inputs (package-propagated-inputs python2-genenetwork2))) - `(,@(fold - alist-delete inputs - (map car - (filter (lambda (x) - (let ((name (car x))) - (or (string-prefix? "python2" name) - (string-prefix? "python-2" name) - (string=? "python" name)))) - inputs))) - ("genenetwork3" ,genenetwork3) - ("parallel" ,parallel) ;; GNU parallel - ("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-elasticsearch" ,python-elasticsearch) - ("python-htmlgen" ,python-htmlgen) - ("python-jinja2" ,python-jinja2) - ("python-sqlalchemy" ,python-sqlalchemy) - ("python-flask-sqlalchemy" ,python-flask-sqlalchemy) - ("python-setuptools" ,python-setuptools) - ("python-scipy" ,python-scipy) - ("python-lxml" ,python-lxml) - ("python-mechanize" ,python-mechanize) - ("python-mysqlclient" ,python-mysqlclient) - ("python-mypy" ,python-mypy) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-parameterized" ,python-parameterized) - ("python-passlib" ,python-passlib) - ("python-pylint" ,python-pylint) - ("python-redis" ,python-redis) - ("python-requests" ,python-requests) - ("python-simplejson" ,python-simplejson) - ("python-pyyaml" ,python-pyyaml) - ("python-markdown" ,python-markdown) - ("python-rdflib" ,python-rdflib) - ;; TODO: Get rid of Python R bindings - ("python-rpy2" ,python-rpy2-next) - ("python-beautifulsoup4" ,python-beautifulsoup4) - ;; Disable for now. Build fails on Penguin2 - ;; ("python-flask-socketio" ,python-flask-socketio) - ("python-xlsxwriter" ,python-xlsxwriter)))) + `(("genenetwork3" ,genenetwork3) + ("parallel" ,parallel) ;; GNU parallel + ("coreutils" ,coreutils) + ("git" ,git) + ("which" ,which) + ("grep" ,grep) + ("r" ,r) + ("r-ctl" ,r-ctl) + ; ("r-phewas" ,r-phewas) + ("r-qtl" ,r-qtl) + ("r-wgcna" ,r-wgcna) + ("redis" ,redis) + ("mariadb" ,mariadb) + ("gemma" ,gemma-gn2) + ("gemma-wrapper" ,gemma-wrapper) + ; ("genenetwork2-files-small" ,genenetwork2-files-small) + ("plink-ng-gn" ,plink-ng-gn) + ; ("pylmm-gn2" ,pylmm-gn2) + ("rust-qtlreaper" ,rust-qtlreaper) + ("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-elasticsearch" ,python-elasticsearch) + ("python-htmlgen" ,python-htmlgen) + ("python-jinja2" ,python-jinja2) + ("python-sqlalchemy" ,python-sqlalchemy) + ("python-flask-sqlalchemy" ,python-flask-sqlalchemy) + ("python-setuptools" ,python-setuptools) + ("python-scipy" ,python-scipy) + ("python-lxml" ,python-lxml) + ("python-mechanize" ,python-mechanize) + ("python-mysqlclient" ,python-mysqlclient) + ("python-mypy" ,python-mypy) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-parameterized" ,python-parameterized) + ("python-passlib" ,python-passlib) + ("python-pylint" ,python-pylint) + ("python-redis" ,python-redis) + ("python-requests" ,python-requests) + ("python-simplejson" ,python-simplejson) + ("python-pyyaml" ,python-pyyaml) + ("python-markdown" ,python-markdown) + ("python-rdflib" ,python-rdflib) + ("python-twint" ,python-twint) + ("python-unittest2" ,python-unittest2) + ;; TODO: Get rid of Python R bindings + ("python-rpy2" ,python-rpy2-next) + ("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-font-awesome" ,javascript-font-awesome))) + (inputs + `(("javascript-colorbox" ,(package-source javascript-colorbox)))) + (build-system python-build-system) (arguments - (let ((python (specification->package "python-wrapper")) - (args (package-arguments python2-genenetwork2))) - (substitute-keyword-arguments args - ((#:python _) python) - ((#:phases phases) - `(modify-phases ,phases - (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 'install 'generate-graph - (lambda* (#:key inputs outputs #:allow-other-keys) - (call-with-output-file - (string-append - (assoc-ref outputs "out") - "/lib/python3.8/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/python3.8/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))))) - (add-after 'install 'generate-dependency-file - (lambda* (#:key inputs outputs #:allow-other-keys) - (call-with-output-file - (string-append - (assoc-ref outputs "out") - "/lib/python3.8/site-packages" - "/wqflask/DEPENDENCIES.md") - (lambda (port) - (format - port " + `(#:python python-wrapper + #:tests? #f ; no 'setup.py test' + #:phases %standard-phases + (modify-phases ,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* '("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/python3.8/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/python3.8/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))))) + (add-after 'install 'generate-dependency-file + (lambda* (#:key inputs outputs #:allow-other-keys) + (call-with-output-file + (string-append + (assoc-ref outputs "out") + "/lib/python3.8/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)))))))))))))))) + ,(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+)))) ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x |