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(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 gnu)
#:use-module (gn packages graphviz)
#:use-module (gn packages javascript)
#:use-module (gn packages maths)
#:use-module (gnu packages python)
#:use-module (gnu packages statistics)
#: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 gnu-build-system)
(arguments
`(#:tests? #f ; no test suite
#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-after 'patch-source-shebangs 'patch--more-shebangs
(lambda* (#:key inputs #:allow-other-keys)
(let* ((bash (assoc-ref inputs "bash"))
(graphviz (assoc-ref inputs "graphviz"))
(octave (assoc-ref inputs "octave"))
(python (assoc-ref inputs "python"))
(rmath (assoc-ref inputs "rmath"))
(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/"))
(for-each (lambda (file)
(patch-shebang file
(list (string-append bash "/bin")
(string-append octave "/bin")
(string-append python "/bin"))))
(find-files "." ".*"))
(substitute*
(append '("home.php")
(find-files "sourcecodes" ".php")
(find-files "sourcecodes/run_scripts" ".*"))
(("/usr/bin/dot") (string-append graphviz "/bin/dot")))
(substitute* "sourcecodes/build.sh"
(("./localscore/libRmath.so") (string-append rmath "/lib/libRmath.so")))
(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))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(delete-file "sourcecodes/localscore/libRmath.so")
(copy-recursively "." out))
#t))
(replace 'build
(lambda _
(with-directory-excursion "sourcecodes"
(substitute* "build.sh"
(("./localscore") "localscore"))
(chmod "k-best/src/buildk_poster.sh" #o755)
(invoke "sh" "build.sh")))))))
(inputs
`(("graphviz" ,graphviz-2.26)
("octave" ,octave-3.4.3)
("python" ,python-2)
("rmath" ,rmath-standalone) ; Should this be r-minimal? Which version?
("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+)))))
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