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| -rw-r--r-- | gn/packages/genenetwork.scm | 158 |
1 files changed, 158 insertions, 0 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index e3e478b..27c583e 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -444,6 +444,164 @@ implemented, light on server resource usage, and fairly speedy.") (description "Genenetwork installation sumo.") (license license:agpl3+)))) +(define-public python3-genenetwork2 + (let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd") + (S specification->package)) + (package + (name "python3-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") + ;; (url "https://github.com/genenetwork/genenetwork2_diet.git") + (commit commit))) + (file-name (string-append name "-" version)) + (sha256 + (base32 + "0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz")))) + (propagated-inputs + `(;; propagated for development purposes + ("python" ,python) ;; probably superfluous + ("coreutils" ,coreutils) + ("git" ,git) + ("vim" ,vim) + ("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) + ("plink-ng-gn" ,plink-ng-gn) + ("rust-qtlreaper" ,rust-qtlreaper) + ("nginx" ,nginx) + ("python-twint" ,python-twint) + ("python-flask" ,python-flask) + ("gunicorn" ,gunicorn) + ("python-pillow" ,python-pillow) + ;; ("python2-pil1" ,python2-pil1-gn) + ("python2-piddle-gn" ,python2-piddle-gn) ; DEPRECATED + ("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) + ("python2-numarray" ,python2-numarray) ; DEPRECATED + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python2-parallel" ,python2-parallel) ; TODO + ("python-parameterized" ,python-parameterized) + ("python-passlib" ,python-passlib) + ("python-redis" ,python-redis) + ("python-requests" ,python-requests) + ("python2-rpy2" ,python2-rpy2) ; TODO + ("python-simplejson" ,python-simplejson) + ("python-pyyaml" ,python-pyyaml) + ("python-unittest2" ,python-unittest2) + ("python-xlsxwriter" ,python-xlsxwriter) + ("python2-qtlreaper" ,python2-qtlreaper) ; Deprecated + ;; All the external js dependencies + ("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-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-async" ,javascript-zxcvbn-async) + ("javascript-jquery-ui" ,javascript-jquery-ui) + ("javascript-jquery-cookie" ,javascript-jquery-cookie) + )) + (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+)))) + ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x |