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-rw-r--r--gn/packages/genenetwork.scm168
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