Merge branch 'master' of http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics

1 files changed, 91 insertions, 49 deletions

diff --git a/gn/packages/bnw.scm b/gn/packages/bnw.scm
index 5c97eab..043077d 100644
--- a/gn/packages/bnw.scm
+++ b/gn/packages/bnw.scm
@@ -14,7 +14,7 @@
 
 (define-public bnw
   (let ((commit "eb6b002b924694808384f1a8d7c6d1121806ae04")
-        (revision "5"))
+        (revision "6"))
     (package
       (name "bnw")
       (version (git-version "1.22" revision commit)) ; June 28, 2019
@@ -86,59 +86,101 @@
                    (("rmdir ") (string-append (which "rmdir") " "))
                    (("wc ") (string-append (which "wc") " ")))
                #t)))
-           ;(add-after 'patch-source-shebangs 'replace-javascript
-           ;  (lambda* (#:key inputs #:allow-other-keys)
-           ;    (let (
-           ;          (jquery        (assoc-ref inputs "jquery"))
-           ;          (awesome       (assoc-ref inputs "awesome"))
-           ;          (cyto          (assoc-ref inputs "cytoscape"))
-           ;          (cyto2         (assoc-ref inputs "cytoscape-2"))
-           ;          (cs-dagre      (assoc-ref inputs "cyto-dagre"))
-           ;          (d3js          (assoc-ref inputs "d3js"))
-           ;          (d3js-multi    (assoc-ref inputs "d3js-multi"))
-           ;          (dagre         (assoc-ref inputs "dagre"))
-           ;          (lodash        (assoc-ref inputs "lodash"))
-           ;          (canvas-toblob (assoc-ref inputs "canvas-toblob"))
-           ;          (filesaver     (assoc-ref inputs "filesaver"))
-           ;          (panzoom       (assoc-ref inputs "panzoom"))
-           ;          (js-path "/share/genenetwork2/javascript/")
-           ;          )
-                 ;(substitute* "sourcecodes/layout_cyto.php"
-                 ;  (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.7.1/cytoscape.min.js")
-                 ;   (string-append cyto js-path "cytoscape/cytoscape.min.js"))
-                 ;  (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape/2.7.29/cytoscape.min.js")
-                 ;   (string-append cyto2 js-path "cytoscape/cytoscape.min.js"))
-                 ;  (("http://spades.bioinf.spbau.ru/~alla/graph_viewer/js/cytoscape-dagre.js")
-                 ;   (string-append cs-dagre js-path "cytoscape-dagre/cytoscape-dagre.js"))
-                 ;  (("https://unpkg.com/dagre@0.7.4/dist/dagre.js")
-                 ;   (string-append dagre js-path "dagre/dagre.js"))
-                 ;  (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape.js-panzoom.css")
-                 ;   (string-append panzoom js-path "cytoscape-panzoom/cytoscape.js-panzoom.css"))
-                 ;  (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape-panzoom.js")
-                 ;   (string-append panzoom js-path "cytoscape-panzoom/cytoscape-panzoom.js"))
-                 ;  (("https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.0.3/css/font-awesome.css")
-                 ;   (string-append awesome "/share/web/font-awesome/css/font-awesome.css"))
-                 ;  (("https://ajax.googleapis.com/ajax/libs/jquery/3.1.0/jquery.min.js")
-                 ;   (string-append jquery "/share/web/jquery/jquery.min.js"))
-                 ;  (("https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.10/lodash.js")
-                 ;   (string-append lodash js-path "lodash/lodash.js")))
-                 ;(substitute* '("sourcecodes/layout_svg_wt.php"
-                 ;               "sourcecodes/layout_svg_no.php")
-                 ;  (("http://d3js.org/d3.v4.min.js")
-                 ;   (string-append d3js js-path "d3js/d3.min.js"))
-                 ;  (("http://d3js.org/d3-selection-multi.v1.js")
-                 ;   (string-append d3js-multi js-path "d3js-multi/d3-selection-multi.js"))
-                 ;  (("https://cdn.rawgit.com/eligrey/canvas-toBlob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toBlob.js")
-                 ;   (string-append canvas-toblob js-path "canvas-toBlob/canvas-toBlob.js"))
-                 ;  (("https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js")
-                 ;   (string-append filesaver js-path "filesaver/filesaver.js")))
-           ;      )
-           ;    #t))
+           (add-after 'patch-source-shebangs 'replace-javascript
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((jquery        (assoc-ref inputs "jquery"))
+                     (awesome       (assoc-ref inputs "awesome"))
+                     (cyto          (assoc-ref inputs "cytoscape"))
+                     (cyto2         (assoc-ref inputs "cytoscape-2"))
+                     (cs-dagre      (assoc-ref inputs "cyto-dagre"))
+                     (d3js          (assoc-ref inputs "d3js"))
+                     (d3js-multi    (assoc-ref inputs "d3js-multi"))
+                     (dagre         (assoc-ref inputs "dagre"))
+                     (lodash        (assoc-ref inputs "lodash"))
+                     (canvas-toblob (assoc-ref inputs "canvas-toblob"))
+                     (filesaver     (assoc-ref inputs "filesaver"))
+                     (panzoom       (assoc-ref inputs "panzoom"))
+                     (js-path "/share/genenetwork2/javascript/"))
+                 (substitute* "sourcecodes/layout_cyto.php"
+                   (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.7.1/cytoscape.min.js")
+                    "/javascript/cytoscape.min.js")
+                   (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape/2.7.29/cytoscape.min.js")
+                    "/javascript/cytoscape2.min.js")
+                   (("http://spades.bioinf.spbau.ru/~alla/graph_viewer/js/cytoscape-dagre.js")
+                    "/javascript/cytoscape-dagre.js")
+                   (("https://unpkg.com/dagre@0.7.4/dist/dagre.js")
+                    "/javascript/dagre.js")
+                   (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape.js-panzoom.css")
+                    "/javascript/cytoscape.js-panzoom.css")
+                   (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape-panzoom.js")
+                    "/javascript/cytoscape-panzoom.js")
+                   (("https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.0.3/css/font-awesome.css")
+                    "/javascript/font-awesome.css")
+                   (("https://ajax.googleapis.com/ajax/libs/jquery/3.1.0/jquery.min.js")
+                    "/javascript/jquery.min.js")
+                   (("https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.10/lodash.js")
+                    "/javascript/lodash.js"))
+                 (substitute* '("sourcecodes/layout_svg_wt.php"
+                                "sourcecodes/layout_svg_no.php")
+                   (("http://d3js.org/d3.v4.min.js")
+                    "/javascript/d3.min.js")
+                   (("http://d3js.org/d3-selection-multi.v1.js")
+                    "/javascript/d3-selection-multi.js")
+                   (("https://cdn.rawgit.com/eligrey/canvas-toBlob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toBlob.js")
+                    "/javascript/canvas-toBlob.js")
+                   (("https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js")
+                    "/javascript/filesaver.js")))
+               #t))
            (replace 'install
              (lambda* (#:key outputs #:allow-other-keys)
                (let ((out (assoc-ref outputs "out")))
                  (copy-recursively "." out))
                #t))
+           (add-after 'install 'install-javascript-libraries
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (let ((out (assoc-ref outputs "out"))
+                     (jquery        (assoc-ref inputs "jquery"))
+                     (awesome       (assoc-ref inputs "awesome"))
+                     (cyto          (assoc-ref inputs "cytoscape"))
+                     (cyto2         (assoc-ref inputs "cytoscape-2"))
+                     (cs-dagre      (assoc-ref inputs "cyto-dagre"))
+                     (d3js          (assoc-ref inputs "d3js"))
+                     (d3js-multi    (assoc-ref inputs "d3js-multi"))
+                     (dagre         (assoc-ref inputs "dagre"))
+                     (lodash        (assoc-ref inputs "lodash"))
+                     (canvas-toblob (assoc-ref inputs "canvas-toblob"))
+                     (filesaver     (assoc-ref inputs "filesaver"))
+                     (panzoom       (assoc-ref inputs "panzoom"))
+                     (js-path  "/share/genenetwork/javascript/")
+                     (js-path2 "/share/genenetwork2/javascript/"))
+                 (mkdir-p (string-append out "/javascript"))
+                 (symlink (string-append (string-append cyto2 js-path2 "cytoscape/cytoscape.min.js"))
+                          (string-append out "/javascript/cytoscape.min.js"))
+                 (symlink (string-append (string-append cyto js-path2 "cytoscape/cytoscape.min.js"))
+                          (string-append out "/javascript/cytoscape2.min.js"))
+                 (symlink (string-append cs-dagre js-path2 "cytoscape-dagre/cytoscape-dagre.js")
+                          (string-append out "/javascript/cytoscape-dagre.js"))
+                 (symlink (string-append dagre js-path2 "dagre/dagre.js")
+                          (string-append out "/javascript/dagre.js"))
+                 (symlink (string-append panzoom js-path2 "cytoscape-panzoom/cytoscape.js-panzoom.css")
+                          (string-append out "/javascript/cytoscape.js-panzoom.css"))
+                 (symlink (string-append panzoom js-path2 "cytoscape-panzoom/cytoscape-panzoom.js")
+                          (string-append out "/javascript/cytoscape-panzoom.js"))
+                 (symlink (string-append awesome "/share/web/font-awesomecss/font-awesome.css")
+                          (string-append out "/javascript/font-awesome.css"))
+                 (symlink (string-append jquery "/share/web/jquery/jquery.min.js")
+                          (string-append out "/javascript/jquery.min.js"))
+                 (symlink (string-append lodash js-path2 "lodash/lodash.js")
+                          (string-append out "/javascript/lodash.js"))
+                 (symlink (string-append d3js js-path "d3js/d3.min.js")
+                          (string-append out "/javascript/d3.min.js"))
+                 (symlink (string-append d3js-multi js-path "d3js-multi/d3-selection-multi.js")
+                          (string-append out "/javascript/d3-selection-multi.js"))
+                 (symlink (string-append canvas-toblob js-path "canvas-toblob/canvas-toBlob.js")
+                          (string-append out "/javascript/canvas-toBlob.js"))
+                 (symlink (string-append filesaver js-path2 "filesaver/FileSaver.js")
+                          (string-append out "/javascript/filesaver.js"))
+               #t)))
            (add-after 'install 'make-files-executable
              (lambda* (#:key outputs #:allow-other-keys)
                (let ((out (assoc-ref outputs "out")))