gn: Adjust genenetwork2 for removal of python2-genenetwork2

1 files changed, 232 insertions, 155 deletions

diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 4c3ef26..60173a9 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -293,7 +293,6 @@ Graphical Fragment Assembly} files and related formats.")
 (define-public genenetwork2
   (let ((commit "84cbf35adbb15c79638372d108308edb05f12683"))
     (package
-      (inherit python2-genenetwork2)
       (name "genenetwork2")
       (version (string-append "3.11-guix-" (string-take commit 7) ))
       (source (origin
@@ -308,166 +307,244 @@ Graphical Fragment Assembly} files and related formats.")
       (native-inputs
        `(("graphviz" ,graphviz)))
       (propagated-inputs
-       (let ((inputs (package-propagated-inputs python2-genenetwork2)))
-         `(,@(fold
-              alist-delete inputs
-              (map car
-                   (filter (lambda (x)
-                             (let ((name (car x)))
-                               (or (string-prefix? "python2" name)
-                                   (string-prefix? "python-2" name)
-                                   (string=? "python" name))))
-                           inputs)))
-           ("genenetwork3" ,genenetwork3)
-           ("parallel" ,parallel) ;; GNU parallel
-           ("python" ,python-wrapper)
-           ("python-pillow" ,python-pillow)
-           ("python-coverage" ,python-coverage)
-           ("python-configparser" ,python-configparser) ;; maintenance/scripts
-           ("python-flask" ,python-flask)
-           ("gunicorn" ,gunicorn)
-           ("python-autopep8" ,python-autopep8)
-           ("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-mypy" ,python-mypy)
-           ("python-numpy" ,python-numpy)
-           ("python-pandas" ,python-pandas)
-           ("python-parameterized" ,python-parameterized)
-           ("python-passlib" ,python-passlib)
-           ("python-pylint" ,python-pylint)
-           ("python-redis" ,python-redis)
-           ("python-requests" ,python-requests)
-           ("python-simplejson" ,python-simplejson)
-           ("python-pyyaml" ,python-pyyaml)
-           ("python-markdown" ,python-markdown)
-           ("python-rdflib" ,python-rdflib)
-           ;; TODO: Get rid of Python R bindings
-           ("python-rpy2" ,python-rpy2-next)
-           ("python-beautifulsoup4" ,python-beautifulsoup4)
-           ;; Disable for now. Build fails on Penguin2
-           ;; ("python-flask-socketio" ,python-flask-socketio)
-           ("python-xlsxwriter" ,python-xlsxwriter))))
+       `(("genenetwork3" ,genenetwork3)
+         ("parallel" ,parallel) ;; GNU parallel
+         ("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" ,python-wrapper)
+         ("python-pillow" ,python-pillow)
+         ("python-coverage" ,python-coverage)
+         ("python-configparser" ,python-configparser) ;; maintenance/scripts
+         ("python-flask" ,python-flask)
+         ("gunicorn" ,gunicorn)
+         ("python-autopep8" ,python-autopep8)
+         ("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-mypy" ,python-mypy)
+         ("python-numpy" ,python-numpy)
+         ("python-pandas" ,python-pandas)
+         ("python-parameterized" ,python-parameterized)
+         ("python-passlib" ,python-passlib)
+         ("python-pylint" ,python-pylint)
+         ("python-redis" ,python-redis)
+         ("python-requests" ,python-requests)
+         ("python-simplejson" ,python-simplejson)
+         ("python-pyyaml" ,python-pyyaml)
+         ("python-markdown" ,python-markdown)
+         ("python-rdflib" ,python-rdflib)
+         ("python-twint" ,python-twint)
+         ("python-unittest2" ,python-unittest2)
+         ;; TODO: Get rid of Python R bindings
+         ("python-rpy2" ,python-rpy2-next)
+         ("python-beautifulsoup4" ,python-beautifulsoup4)
+         ;; Disable for now. Build fails on Penguin2
+         ;; ("python-flask-socketio" ,python-flask-socketio)
+         ("python-xlsxwriter" ,python-xlsxwriter)
+         ;; 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
-       (let ((python (specification->package "python-wrapper"))
-             (args (package-arguments python2-genenetwork2)))
-         (substitute-keyword-arguments args
-           ((#:python _) python)
-           ((#:phases phases)
-            `(modify-phases ,phases
-               (add-after 'unpack 'fix-paths-scripts
-                 (lambda _
-                   (substitute* "bin/genenetwork2"
-                     (("/usr/bin/env") (which "env"))
-                     (("python ") (string-append (which "python3") " "))
-                     (("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")))
-                   #t))
-               (add-after 'install 'generate-graph
-                 (lambda* (#:key inputs outputs #:allow-other-keys)
-                   (call-with-output-file
-                       (string-append
-                        (assoc-ref outputs "out")
-                        "/lib/python3.8/site-packages"
-                        "/wqflask/dependency-graph.html")
-                     (lambda (port)
-                       (format
-                        port "~a"
-                        ,(call-with-output-string
-                           (lambda (p)
-                             (with-output-to-port p
-                               (lambda ()
-                                 (run-with-store
-                                     (open-connection)
-                                   (export-graph
-                                    (list this-package)
-                                    p
-                                    #:node-type %package-node-type
-                                    #:backend %d3js-backend)))))))))))
-               (add-after 'install 'generate-dag-svg-file
-                 (lambda* (#:key inputs outputs #:allow-other-keys)
-                   (let* ((output-dir
-                           (string-append
-                            (assoc-ref outputs "out")
-                            "/lib/python3.8/site-packages/wqflask/"))
-                          (dot-file
-                           (string-append
-                            output-dir
-                            "dependency-graph.dot"))
-                          (svg-file
-                           (string-append
-                            output-dir
-                            "dependency-graph.svg")))
-                     (begin
-                       (call-with-output-file
-                           dot-file
-                         (lambda (port)
-                           (format
-                            port "~a"
-                            ,(call-with-output-string
-                               (lambda (p)
-                                 (with-output-to-port p
-                                   (lambda ()
-                                     (run-with-store
-                                         (open-connection)
-                                       (export-graph
-                                        (list this-package)
-                                        p
-                                        #:node-type %package-node-type
-                                        #:backend %graphviz-backend)))))))))
-                       (invoke "dot" "-Tsvg" "-o" svg-file dot-file)))))
-               (add-after 'install 'generate-dependency-file
-                 (lambda* (#:key inputs outputs #:allow-other-keys)
-                   (call-with-output-file
-                       (string-append
-                        (assoc-ref outputs "out")
-                        "/lib/python3.8/site-packages"
-                        "/wqflask/DEPENDENCIES.md")
-                     (lambda (port)
-                       (format
-                        port "
+       `(#:python python-wrapper
+         #:tests? #f        ; no 'setup.py test'
+         #:phases %standard-phases
+         (modify-phases ,phases
+            (delete 'reset-gzip-timestamps)
+            (add-after 'unpack 'fix-paths-scripts
+              (lambda _
+                (substitute* "bin/genenetwork2"
+                  (("/usr/bin/env") (which "env"))
+                  (("python ") (string-append (which "python3") " "))
+                  (("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")))
+                #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" ))
+                    )
+                  )))
+            (add-after 'install 'generate-graph
+              (lambda* (#:key inputs outputs #:allow-other-keys)
+                (call-with-output-file
+                    (string-append
+                     (assoc-ref outputs "out")
+                     "/lib/python3.8/site-packages"
+                     "/wqflask/dependency-graph.html")
+                  (lambda (port)
+                    (format
+                     port "~a"
+                     ,(call-with-output-string
+                        (lambda (p)
+                          (with-output-to-port p
+                            (lambda ()
+                              (run-with-store
+                                  (open-connection)
+                                (export-graph
+                                 (list this-package)
+                                 p
+                                 #:node-type %package-node-type
+                                 #:backend %d3js-backend)))))))))))
+            (add-after 'install 'generate-dag-svg-file
+              (lambda* (#:key inputs outputs #:allow-other-keys)
+                (let* ((output-dir
+                        (string-append
+                         (assoc-ref outputs "out")
+                         "/lib/python3.8/site-packages/wqflask/"))
+                       (dot-file
+                        (string-append
+                         output-dir
+                         "dependency-graph.dot"))
+                       (svg-file
+                        (string-append
+                         output-dir
+                         "dependency-graph.svg")))
+                  (begin
+                    (call-with-output-file
+                        dot-file
+                      (lambda (port)
+                        (format
+                         port "~a"
+                         ,(call-with-output-string
+                            (lambda (p)
+                              (with-output-to-port p
+                                (lambda ()
+                                  (run-with-store
+                                      (open-connection)
+                                    (export-graph
+                                     (list this-package)
+                                     p
+                                     #:node-type %package-node-type
+                                     #:backend %graphviz-backend)))))))))
+                    (invoke "dot" "-Tsvg" "-o" svg-file dot-file)))))
+            (add-after 'install 'generate-dependency-file
+              (lambda* (#:key inputs outputs #:allow-other-keys)
+                (call-with-output-file
+                    (string-append
+                     (assoc-ref outputs "out")
+                     "/lib/python3.8/site-packages"
+                     "/wqflask/DEPENDENCIES.md")
+                  (lambda (port)
+                    (format
+                     port "
 #### System Inputs (generated from ~a package defined in ~a)
 |Name | Description |
 |-----|-------------|
 ~a
 "
-                        ,(package-name this-package)
-                        (string-append
-                         "[genenetwork.scm]"
-                         "(http://git.genenetwork.org/"
-                         "guix-bioinformatics/guix-bioinformatics"
-                         "/src/branch/master/gn/packages/"
-                         "genenetwork.scm)")
-                        ,(apply
-                          string-append
-                          (map
-                           (lambda (input)
-                             (let* ((pkg (cadr input))
-                                    (name (package-name pkg))
-                                    (version (package-version pkg))
-                                    (home-page (package-home-page pkg))
-                                    (description (package-synopsis pkg)))
-                               (string-append
-                                "| **[" name "](" home-page ")** v"
-                                version"| "
-                                description " |\n")))
-                           (package-propagated-inputs this-package))))))))))))))))
+                     ,(package-name this-package)
+                     (string-append
+                      "[genenetwork.scm]"
+                      "(http://git.genenetwork.org/"
+                      "guix-bioinformatics/guix-bioinformatics"
+                      "/src/branch/master/gn/packages/"
+                      "genenetwork.scm)")
+                     ,(apply
+                       string-append
+                       (map
+                        (lambda (input)
+                          (let* ((pkg (cadr input))
+                                 (name (package-name pkg))
+                                 (version (package-version pkg))
+                                 (home-page (package-home-page pkg))
+                                 (description (package-synopsis pkg)))
+                            (string-append
+                             "| **[" name "](" home-page ")** v"
+                             version"| "
+                             description " |\n")))
+                        (package-propagated-inputs this-package)))))))))))
+      (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