diff options
Diffstat (limited to 'gn/packages/bnw.scm')
| -rw-r--r-- | gn/packages/bnw.scm | 118 |
1 files changed, 118 insertions, 0 deletions
diff --git a/gn/packages/bnw.scm b/gn/packages/bnw.scm new file mode 100644 index 0000000..2c34256 --- /dev/null +++ b/gn/packages/bnw.scm @@ -0,0 +1,118 @@ +(define-module (gn packages bnw) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix git-download) + #: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 (gn packages web)) + +(define-public bnw + (let ((commit "eb6b002b924694808384f1a8d7c6d1121806ae04") + (revision "1")) + (package + (name "bnw") + (version (git-version "1.22" revision commit)) ; June 28, 2019 + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ziejd2/BNW.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10qwykp2zcyxih6a52icvy30ps69qk4v3jgirmdpw1l15zi4p2wq")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (source (assoc-ref %build-inputs "source")) + (bash (assoc-ref %build-inputs "bash")) + (graphviz (assoc-ref %build-inputs "graphviz")) + (octave (assoc-ref %build-inputs "octave")) + (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 + (list (string-append bash "/bin") + (string-append octave "/bin") + (string-append python "/bin")))) + (find-files out ".*")) + (with-directory-excursion out + (substitute* + (append '("home.php") + (find-files "sourcecodes" ".php") + (find-files "sourcecodes/run_scripts" ".*")) + (("/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) + ("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).") + (license (list license:gpl2 + license:gpl2+ + license:lgpl2.1+))))) |