diff options
Diffstat (limited to 'gn/packages/genenetwork.scm')
| -rw-r--r-- | gn/packages/genenetwork.scm | 168 |
1 files changed, 0 insertions, 168 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 45bae18..4c3ef26 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -175,11 +175,6 @@ Gunicorn server is broadly compatible with various web frameworks, simply implemented, light on server resource usage, and fairly speedy.") (license license:expat))) - -(define-public python2-gunicorn-gn - (package-with-python2 python-gunicorn-gn)) - - (define-public rust-qtlreaper (let ((commit "2e7fed6d45b0b602d80fa2a55835f96ef1cba9e3") (revision "1")) @@ -254,169 +249,6 @@ implemented, light on server resource usage, and fairly speedy.") Graphical Fragment Assembly} files and related formats.") (license license:expat))) -(define-public python2-genenetwork2 - (let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd")) - (package - (name "python2-genenetwork2") - (version (string-append "2.11-guix-" (string-take commit 7) )) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://pjotrp@gitlab.com/genenetwork/gn2_diet.git") - (commit commit))) - (file-name (string-append name "-" version)) - (sha256 - (base32 - "0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz")))) - (propagated-inputs - `(;; propagated for development purposes - ("python" ,python-2) ;; probably superfluous - ("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-twint" ,python-twint) - ("python2-coverage" ,python2-coverage) - ("python2-flask" ,python2-flask) - ("python2-gunicorn-gn" ,python2-gunicorn-gn) - ("python2-pillow" ,python2-pillow) ;; - for later! - ("python2-pil1" ,python2-pil1-gn) - ("python2-piddle-gn" ,python2-piddle-gn) - ("python2-cssselect" ,python2-cssselect) - ("python2-elasticsearch" ,python2-elasticsearch) - ; ("python2-htmlgen" ,python2-htmlgen) - ("python2-htmlgen-gn" ,python2-htmlgen-gn) - ("python2-jinja2" ,python2-jinja2) - ("python2-sqlalchemy" ,python2-sqlalchemy) - ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy) - ("python2-setuptools" ,python2-setuptools) - ("python2-scipy" ,python2-scipy) - ("python2-lxml" ,python2-lxml) - ("python2-mechanize" ,python2-mechanize) - ("python2-mock" ,python2-mock) - ("python2-mysqlclient" ,python2-mysqlclient) - ("python2-nose" ,python-nose2) - ("python2-numarray" ,python2-numarray) - ("python2-numpy" ,python2-numpy) - ("python2-pandas" ,python2-pandas) - ("python2-parallel" ,python2-parallel) - ("python2-parameterized" ,python2-parameterized) - ("python2-passlib" ,python2-passlib) - ("python2-redis" ,python2-redis) - ("python2-requests" ,python2-requests) - ("python2-rpy2" ,python2-rpy2) - ("python2-simplejson" ,python2-simplejson) - ("python2-pyyaml" ,python2-pyyaml) - ("python-unittest2" ,python-unittest2) - ("python2-xlsxwriter" ,python2-xlsxwriter) - ("python2-qtlreaper" ,python2-qtlreaper) - ;; 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 - `(#:python ,python-2 - #: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 "python2") " ")) - (("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")) ; three whiches in a row! - ) - #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" )) - ) - )))) - #:tests? #f)) ; no 'setup.py test' - (home-page "http://genenetwork.org/") - (synopsis "Full genenetwork services") - (description "Genenetwork installation sumo.") - (license license:agpl3+)))) - (define-public genenetwork3 (let ((commit "487e50e8f8304a65e7af3759c13256f921efb8be")) (package |