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authorEfraim Flashner2019-07-22 06:49:20 -0500
committerEfraim Flashner2019-07-22 07:50:37 -0500
commit65d03f34c36d2e83a6c63de1f8fa9a8f91f90b35 (patch)
tree0acbe6762a8d12a29e7a10be06933acba730a29b /gn
parent6c708ab87fbb58ffd904b1b02087e38a6f39933a (diff)
downloadguix-bioinformatics-65d03f34c36d2e83a6c63de1f8fa9a8f91f90b35.tar.gz
gn: bnw: Add javascript libraries.
* gn/packages/bnw.scm (bnw)[inputs]: Add web-jquery, web-font-awesome, javascript-cytoscape, javascript-cytoscape-2, javascript-dagre, javascript-lodash, javascript-cytoscape-dagre, javascript-cytoscape-panzoom, javascript-d3js-4, javascript-d3js-multi, javascript-canvas-toblob, javascript-filesaver. [arguments]: Add references to new inputs.
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bnw.scm64
1 files changed, 60 insertions, 4 deletions
diff --git a/gn/packages/bnw.scm b/gn/packages/bnw.scm
index e09a9a3..2c34256 100644
--- a/gn/packages/bnw.scm
+++ b/gn/packages/bnw.scm
@@ -5,8 +5,10 @@
#:use-module (guix build-system trivial)
#:use-module (gnu packages bash)
#:use-module (gn packages graphviz)
+ #:use-module (gn packages javascript)
#:use-module (gn packages maths)
- #:use-module (gnu packages python))
+ #:use-module (gnu packages python)
+ #:use-module (gn packages web))
(define-public bnw
(let ((commit "eb6b002b924694808384f1a8d7c6d1121806ae04")
@@ -34,7 +36,20 @@
(bash (assoc-ref %build-inputs "bash"))
(graphviz (assoc-ref %build-inputs "graphviz"))
(octave (assoc-ref %build-inputs "octave"))
- (python (assoc-ref %build-inputs "python")))
+ (python (assoc-ref %build-inputs "python"))
+ (jquery (assoc-ref %build-inputs "jquery"))
+ (awesome (assoc-ref %build-inputs "awesome"))
+ (cyto (assoc-ref %build-inputs "cytoscape"))
+ (cyto2 (assoc-ref %build-inputs "cytoscape-2"))
+ (cs-dagre (assoc-ref %build-inputs "cyto-dagre"))
+ (d3js (assoc-ref %build-inputs "d3js"))
+ (d3js-multi (assoc-ref %build-inputs "d3js-multi"))
+ (dagre (assoc-ref %build-inputs "dagre"))
+ (lodash (assoc-ref %build-inputs "lodash"))
+ (canvas-toblob (assoc-ref %build-inputs "canvas-toblob"))
+ (filesaver (assoc-ref %build-inputs "filesaver"))
+ (panzoom (assoc-ref %build-inputs "panzoom"))
+ (js-path "/share/genenetwork2/javascript/"))
(copy-recursively source out)
(for-each (lambda (file)
(patch-shebang file
@@ -47,13 +62,54 @@
(append '("home.php")
(find-files "sourcecodes" ".php")
(find-files "sourcecodes/run_scripts" ".*"))
- (("/usr/bin/dot") (string-append graphviz "/bin/dot"))))))))
+ (("/usr/bin/dot") (string-append graphviz "/bin/dot")))
+ (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"))))))))
(native-inputs `(("source" ,source)))
(inputs
`(("bash" ,bash-minimal)
("graphviz" ,graphviz-2.26)
("octave" ,octave-3.4.3)
- ("python" ,python-2)))
+ ("python" ,python-2)
+ ("jquery" ,web-jquery)
+ ("awesome" ,web-font-awesome)
+ ("cytoscape" ,javascript-cytoscape)
+ ("cytoscape-2" ,javascript-cytoscape-2)
+ ("d3js" ,javascript-d3js-4)
+ ("d3js-multi" ,javascript-d3js-multi)
+ ("dagre" ,javascript-dagre)
+ ("lodash" ,javascript-lodash)
+ ("canvas-toblob" ,javascript-canvas-toblob)
+ ("filesaver" ,javascript-filesaver)
+ ("cyto-dagre" ,javascript-cytoscape-dagre)
+ ("panzoom" ,javascript-cytoscape-panzoom)))
(home-page "http://compbio.uthsc.edu/BNW/")
(synopsis "Bayesian Network Webserver")
(description "This contains the code for the @dfn{Bayesian Network Webserver} (BNW).")