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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 (gnu packages gcc)
#:use-module (gnu packages python)
#:use-module (gnu packages statistics)
#:use-module (gn packages graphviz)
#:use-module (gn packages javascript)
#:use-module (gn packages maths)
#:use-module (gn packages python)
#:use-module (gn packages web))
(define-public bnw
(let ((commit "eb6b002b924694808384f1a8d7c6d1121806ae04")
(revision "5"))
(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 'unpack 'patch-source
(lambda _
(substitute* "index.html"
(("url=home.php") "url=sourcecodes/home.php"))
(substitute* "home.php"
(("http://bnw.genenetwork.org/BNW_1.22")
"http://bnw-test.genenetwork.org"))
(substitute* "sourcecodes/header_batchsearch.inc"
(("my_style.css") "my_new_style.css"))
(substitute* (find-files "." "\\.php")
(("HTTP_POST_VARS") "_POST")
(("HTTP_POST_FILES") "_FILES"))
;; change $dir to a writable directory
;(substitute* (find-files "sourcecodes" "\\.php$")
; (("\\$dir=\"./data") "$dir=\"./data/tmp"))
#t))
(add-after 'patch-source-shebangs 'patch-more-shebangs
(lambda* (#:key inputs #:allow-other-keys)
(let ((bash (assoc-ref inputs "bash"))
(graphviz (assoc-ref inputs "graphviz"))
(octave (assoc-ref inputs "octave"))
(python (assoc-ref inputs "python"))
(rmath (assoc-ref inputs "rmath")))
(for-each (lambda (file)
(patch-shebang file
(list (string-append bash "/bin")
(string-append octave "/bin")
(string-append python "/bin"))))
(find-files "." ".*"))
(substitute* (find-files "sourcecodes" "(^run|py$)")
(("/home/jziebart/python/Python-2.7.15/python")
(which "python2")))
(substitute*
(append (find-files "sourcecodes" ".php")
(find-files "sourcecodes/run_scripts" ".*"))
(("/usr/bin/dot") (string-append graphviz "/bin/dot")))
(substitute* '("sourcecodes/build.sh"
"downloads/BNW/src/build.sh")
(("./localscore/libRmath.so")
(string-append rmath "/lib/libRmath.so")))
(substitute* (find-files "." "\\.sh$")
(("cat ") (string-append (which "cat") " "))
(("\\ cp") (string-append " " (which "cp")))
(("date ") (string-append (which "date") " "))
(("dirname \\$0") (string-append (which "dirname")" $0"))
(("dirname \"\\$0") (string-append (which "dirname")" \"$0"))
(("expr ") (string-append (which "expr") " "))
(("head ") (string-append (which "head") " "))
(("mkdir ") (string-append (which "mkdir") " "))
(("^rm ") (string-append (which "rm") " "))
(("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))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(copy-recursively "." out))
#t))
(add-after 'install 'make-files-executable
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(for-each
(lambda (file)
(chmod file #o555))
(append (find-files out "\\.(sh|py)$")
(find-files (string-append out "/sourcecodes/run_scripts/" "."))))
;; This folder needs to be writable.
(chmod (string-append out "/sourcecodes/data") #o777)
#t)))
(replace 'build
(lambda _
(with-directory-excursion "sourcecodes"
(substitute* "build.sh"
(("./localscore") "localscore"))
(chmod "k-best/src/buildk_poster.sh" #o555)
(invoke "sh" "build.sh")
;; from info_files/plotly_notes.txt
;(with-directory-excursion "data"
; (setenv "HOME" "/tmp")
; (invoke "python" "../cv_plotly.py" "LvQ")
; (invoke "sh" "../plotly_loo.sh"))
;(invoke "./run_scripts/run_loo" "LvQ Weight")
))))))
(inputs
`(("graphviz" ,graphviz-2.26)
("octave" ,octave-3.4.3)
("plotly" ,python2-plotly-3.2.1)
("python" ,python-2)
("rmath" ,rmath-standalone)
;; the javascript libraries:
("awesome" ,web-font-awesome)
("canvas-toblob" ,javascript-canvas-toblob)
("cyto-dagre" ,javascript-cytoscape-dagre)
("cytoscape" ,javascript-cytoscape)
("cytoscape-2" ,javascript-cytoscape-2)
("d3js" ,javascript-d3js-4)
("d3js-multi" ,javascript-d3js-multi)
("dagre" ,javascript-dagre)
("filesaver" ,javascript-filesaver)
("jquery" ,web-jquery)
("lodash" ,javascript-lodash)
("panzoom" ,javascript-cytoscape-panzoom)))
(native-inputs
`(("gcc" ,gcc-5)))
(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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