python2-genenetwork2: remove unused Python2 version of genenetwork

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