diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/genenetwork.scm | 191 |
1 files changed, 75 insertions, 116 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 8a76327..30f941b 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -43,7 +43,8 @@ #:use-module (gn packages python) #:use-module (gn packages python24) #:use-module (gn packages statistics) - #:use-module (gn packages web)) + #:use-module (gn packages web) + #:use-module (srfi srfi-1)) @@ -446,120 +447,79 @@ implemented, light on server resource usage, and fairly speedy.") (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) - ("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) - ;; 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 + (let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd")) + (package + (inherit genenetwork2) + (name "python3-genenetwork2") + (version (string-append "3.11-guix-" (string-take commit 7) )) + (propagated-inputs + `(,@(fold alist-delete (package-propagated-inputs genenetwork2) + '("python-2" + "python2-coverage" + "python2-flask" + "python2-gunicorn-gn" + "python2-cssselect" + "python2-elasticsearch" + "python2-htmlgen-gn" + "python2-jinja2" + "python2-sqlalchemy" + "python2-flask-sqlalchemy" + "python2-setuptools" + "python2-scipy" + "python2-lxml" + "python2-mechanize" + "python2-mock" + "python2-mysqlclient" + "python2-nose" + "python2-numarray" + "python2-numpy" + "python2-pandas" + "python2-parallel" + "python2-parameterized" + "python2-passlib" + "python2-redis" + "python2-requests" + "python2-simplejson" + "python2-pyyaml" + "python-unittest2" + "python2-xlsxwriter" + "python2-qtlreaper")) + ("python-pillow" ,python-pillow) + ("python-coverage" ,python-coverage) + ("python-flask" ,python-flask) + ("gunicorn" ,gunicorn) + ("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-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-mock" ,python-mock) + ("python-parameterized" ,python-parameterized) + ("python-passlib" ,python-passlib) + ("python-redis" ,python-redis) + ("python-requests" ,python-requests) + ("python-simplejson" ,python-simplejson) + ("python-pyyaml" ,python-pyyaml) + ("python-unittest2" ,python-unittest2) + ("python-xlsxwriter" ,python-xlsxwriter))) + (arguments + `(#:python ,python-3 + #: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") " ")) + (("python ") (string-append (which "python") " ")) (("readlink") (which "readlink")) (("dirname") (which "dirname")) (("basename") (which "basename")) @@ -581,18 +541,17 @@ implemented, light on server resource usage, and fairly speedy.") #t))) (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"))) + (let* ( + (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") (("^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+)))) + #:tests? #f)) ; no 'setup.py test' + ))) ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x |