1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
|
(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 "4"))
(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") "$dir=\"./data/tmp"))
#t))
(add-after 'patch-source-shebangs 'patch-more-shebangs
(lambda* (#:key inputs #:allow-other-keys)
(let* ((bash (assoc-ref inputs "bash"))
(graphviz (assoc-ref inputs "graphviz"))
(octave (assoc-ref inputs "octave"))
(python (assoc-ref inputs "python"))
(rmath (assoc-ref inputs "rmath"))
(jquery (assoc-ref inputs "jquery"))
(awesome (assoc-ref inputs "awesome"))
(cyto (assoc-ref inputs "cytoscape"))
(cyto2 (assoc-ref inputs "cytoscape-2"))
(cs-dagre (assoc-ref inputs "cyto-dagre"))
(d3js (assoc-ref inputs "d3js"))
(d3js-multi (assoc-ref inputs "d3js-multi"))
(dagre (assoc-ref inputs "dagre"))
(lodash (assoc-ref inputs "lodash"))
(canvas-toblob (assoc-ref inputs "canvas-toblob"))
(filesaver (assoc-ref inputs "filesaver"))
(panzoom (assoc-ref inputs "panzoom"))
(js-path "/share/genenetwork2/javascript/"))
(for-each (lambda (file)
(patch-shebang file
(list (string-append bash "/bin")
(string-append octave "/bin")
(string-append python "/bin"))))
(find-files "." ".*"))
(substitute* '("sourcecodes/examplefilecopy.sh"
"sourcecodes/filecopy.sh")
(("^rm") (which "rm"))
(("\\ cp") (string-append " " (which "cp"))))
(substitute* (find-files "sourcecodes" "(^run|py$)")
(("/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* "sourcecodes/run.sh"
(("rm ") (string-append (which "rm") " "))
(("rmdir ") (string-append (which "rmdir") " "))
(("mkdir ") (string-append (which "mkdir") " "))
(("dirname ") (string-append (which "dirname")" ")))
;(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/" "."))))
(chmod (string-append out "/sourcecodes/data") #o777) ; needs to be writable
#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)
("python" ,python-2)
("plotly" ,python2-plotly-3.2.1)
("rmath" ,rmath-standalone)
("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)))
(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+)))))
|
