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@ -175,11 +175,6 @@ Gunicorn server is broadly compatible with various web frameworks, simply |
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implemented, light on server resource usage, and fairly speedy.") |
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(license license:expat))) |
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(define-public python2-gunicorn-gn |
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(package-with-python2 python-gunicorn-gn)) |
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(define-public rust-qtlreaper |
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(let ((commit "2e7fed6d45b0b602d80fa2a55835f96ef1cba9e3") |
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(revision "1")) |
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@ -254,169 +249,6 @@ implemented, light on server resource usage, and fairly speedy.") |
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Graphical Fragment Assembly} files and related formats.") |
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(license license:expat))) |
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(define-public python2-genenetwork2 |
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(let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd")) |
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(package |
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(name "python2-genenetwork2") |
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(version (string-append "2.11-guix-" (string-take commit 7) )) |
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(source (origin |
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(method git-fetch) |
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(uri (git-reference |
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(url "https://pjotrp@gitlab.com/genenetwork/gn2_diet.git") |
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(commit commit))) |
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(file-name (string-append name "-" version)) |
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(sha256 |
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(base32 |
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"0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz")))) |
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(propagated-inputs |
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`(;; propagated for development purposes |
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("python" ,python-2) ;; probably superfluous |
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("coreutils" ,coreutils) |
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("git" ,git) |
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("which" ,which) |
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("grep" ,grep) |
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("r" ,r) |
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("r-ctl" ,r-ctl) |
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; ("r-phewas" ,r-phewas) |
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("r-qtl" ,r-qtl) |
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("r-wgcna" ,r-wgcna) |
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("redis" ,redis) |
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("mariadb" ,mariadb) |
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("gemma" ,gemma-gn2) |
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("gemma-wrapper" ,gemma-wrapper) |
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; ("genenetwork2-files-small" ,genenetwork2-files-small) |
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("plink-ng-gn" ,plink-ng-gn) |
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; ("pylmm-gn2" ,pylmm-gn2) |
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("rust-qtlreaper" ,rust-qtlreaper) |
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("nginx" ,nginx) |
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("python-twint" ,python-twint) |
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("python2-coverage" ,python2-coverage) |
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("python2-flask" ,python2-flask) |
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("python2-gunicorn-gn" ,python2-gunicorn-gn) |
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("python2-pillow" ,python2-pillow) ;; - for later! |
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("python2-pil1" ,python2-pil1-gn) |
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("python2-piddle-gn" ,python2-piddle-gn) |
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("python2-cssselect" ,python2-cssselect) |
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("python2-elasticsearch" ,python2-elasticsearch) |
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; ("python2-htmlgen" ,python2-htmlgen) |
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("python2-htmlgen-gn" ,python2-htmlgen-gn) |
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("python2-jinja2" ,python2-jinja2) |
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("python2-sqlalchemy" ,python2-sqlalchemy) |
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("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy) |
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("python2-setuptools" ,python2-setuptools) |
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("python2-scipy" ,python2-scipy) |
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("python2-lxml" ,python2-lxml) |
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("python2-mechanize" ,python2-mechanize) |
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("python2-mock" ,python2-mock) |
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("python2-mysqlclient" ,python2-mysqlclient) |
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("python2-nose" ,python-nose2) |
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("python2-numarray" ,python2-numarray) |
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("python2-numpy" ,python2-numpy) |
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("python2-pandas" ,python2-pandas) |
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("python2-parallel" ,python2-parallel) |
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("python2-parameterized" ,python2-parameterized) |
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("python2-passlib" ,python2-passlib) |
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("python2-redis" ,python2-redis) |
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("python2-requests" ,python2-requests) |
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("python2-rpy2" ,python2-rpy2) |
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("python2-simplejson" ,python2-simplejson) |
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("python2-pyyaml" ,python2-pyyaml) |
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("python-unittest2" ,python-unittest2) |
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("python2-xlsxwriter" ,python2-xlsxwriter) |
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("python2-qtlreaper" ,python2-qtlreaper) |
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;; All the external js dependencies |
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("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher) |
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("javascript-cytoscape" ,javascript-cytoscape) |
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("javascript-panzoom" ,javascript-cytoscape-panzoom) |
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("javascript-qtip" ,javascript-cytoscape-qtip) |
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("javascript-chroma" ,javascript-chroma) |
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("javascript-d3-tip" ,javascript-d3-tip) |
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("javascript-jscolor" ,javascript-jscolor) |
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("javascript-colorbox" ,javascript-colorbox) |
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("javascript-jszip" ,javascript-jszip) |
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("js-jstat" ,js-jstat) |
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("js-md5" ,js-md5) |
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("js-parsley" ,js-parsley) |
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("javascript-plotly" ,javascript-plotly) |
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("javascript-typeahead" ,javascript-typeahead) |
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("js-underscore" ,js-underscore) |
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("js-smart-time-ago" ,js-smart-time-ago) |
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("javascript-nouislider" ,javascript-nouislider) |
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("javascript-purescript-genome-browser" ,javascript-purescript-genome-browser) |
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("javascript-ckeditor" ,javascript-ckeditor) |
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("javascript-datatables" ,javascript-datatables) |
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("javascript-datatables-scroller" ,javascript-datatables-scroller) |
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("javascript-datatables-buttons" ,javascript-datatables-buttons) |
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("javascript-datatables-buttons-bootstrap" ,javascript-datatables-buttons-bootstrap) |
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("javascript-datatables-plugins" ,javascript-datatables-plugins) |
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("javascript-datatables-col-reorder" ,javascript-datatables-col-reorder) |
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("javascript-datatables-col-resize" ,javascript-datatables-col-resize) |
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("javascript-datatables-buttons-styles" ,javascript-datatables-buttons-styles) |
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("javascript-shapiro-wilk" ,javascript-shapiro-wilk) |
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("javascript-underscore-string" ,javascript-underscore-string) |
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("javascript-qtip2" ,javascript-qtip2) |
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("javascript-d3js" ,javascript-d3js) |
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("javascript-nvd3" ,javascript-nvd3) |
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("javascript-bootstrap" ,javascript-bootstrap) |
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("javascript-jquery" ,javascript-jquery) |
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("javascript-zxcvbn" ,javascript-zxcvbn) |
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("javascript-jquery-ui" ,javascript-jquery-ui) |
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("javascript-jquery-cookie" ,javascript-jquery-cookie) |
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("javascript-font-awesome" ,javascript-font-awesome))) |
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(inputs |
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`(("javascript-colorbox" ,(package-source javascript-colorbox)))) |
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(build-system python-build-system) |
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(arguments |
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`(#:python ,python-2 |
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#:phases |
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(modify-phases %standard-phases |
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(delete 'reset-gzip-timestamps) |
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(add-after 'unpack 'fix-paths-scripts |
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(lambda _ |
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(substitute* "bin/genenetwork2" |
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(("/usr/bin/env") (which "env")) |
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(("python ") (string-append (which "python2") " ")) |
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(("readlink") (which "readlink")) |
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(("dirname") (which "dirname")) |
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(("basename") (which "basename")) |
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(("cat") (which "cat")) |
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(("echo") (which "echo")) |
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(("redis-server") (which "redis-server")) |
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(("git") (which "git")) |
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(("grep") (which "grep")) |
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(("rm") (which "rm")) |
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(("which") (which "which")) ; three whiches in a row! |
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) |
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#t)) |
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(add-after 'unpack 'patch-javascript |
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(lambda* (#:key inputs #:allow-other-keys) |
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(let ((colorbox (assoc-ref inputs "javascript-colorbox")) |
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(gn2 "/share/genenetwork2/javascript/")) |
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(delete-file-recursively "wqflask/wqflask/static/packages/colorbox") |
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(copy-recursively colorbox "wqflask/wqflask/static/packages/colorbox") |
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#t))) |
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(add-before 'install 'fix-paths |
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(lambda* (#:key inputs #:allow-other-keys) |
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(let* ( |
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; (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2")) |
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; (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) |
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(plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) |
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(gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) |
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) |
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(substitute* '("etc/default_settings.py") |
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; (("^GENENETWORK_FILES +=.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) |
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; (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) |
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(("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) |
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(("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )) |
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) |
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)))) |
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#:tests? #f)) ; no 'setup.py test' |
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(home-page "http://genenetwork.org/") |
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(synopsis "Full genenetwork services") |
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(description "Genenetwork installation sumo.") |
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(license license:agpl3+)))) |
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(define-public genenetwork3 |
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(let ((commit "487e50e8f8304a65e7af3759c13256f921efb8be")) |
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(package |
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pjotrp
11 months ago