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
|
(define-module (gn packages ratspub)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix utils)
#:use-module (guix packages)
#:use-module (guix git-download)
#:use-module (guix build-system python)
#:use-module (gnu packages admin)
#:use-module (gnu packages bioinformatics)
#:use-module (gn packages javascript)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gn packages web))
(define-public ratspub
(package
(name "ratspub")
(version "0.3.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/chen42/ratspub.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1ii3721mqd3dbpjkhqi7yqjd9bqcf0g19kdbb8265pmbfjjsg164"))))
(build-system python-build-system)
(arguments
`(#:tests? #f ; no test suite
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(add-after 'unpack 'patch-sources
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(inetutils (assoc-ref inputs "inetutils")))
(substitute* '("templates/cytoscape.html"
"templates/tableview.html"
"templates/tableview0.html"
"templates/userarchive.html")
(("script src=.*")
"script src=\"/static/cytoscape.min.js\"></script>\n"))
(substitute* "templates/layout.html"
(("https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css.*")
"/static/bootstrap.min.css\">\n")
(("https://.*.bootstrapcdn.com/bootstrap/4.*/js/bootstrap.min.js.*")
"/static/bootstrap.min.js\"></script>\n")
(("https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css")
"/static/font-awesome.min.css")
(("https://code.jquery.com/jquery-3.2.1.slim.min.js.*")
"/static/jquery.slim.min.js\"></script>\n")
;(("https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js.*")
; "/static/popper.min.js\"></script>\n")
)
(substitute* "ratspub.py"
(("hostname") (string-append inetutils "/bin/hostname"))))
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(copy-recursively "." out))
#t))
(add-after 'install 'install-javascript
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(awesome (assoc-ref inputs "font-awesome"))
(bootstrap (assoc-ref inputs "bootstrap"))
(cytoscape (assoc-ref inputs "cytoscape"))
(jquery (assoc-ref inputs "jquery"))
;(js-popper (assoc-ref inputs "js-popper"))
)
(symlink (string-append awesome
"/share/web/font-awesomecss/font-awesome.min.css")
(string-append out "/static/font-awesome.min.css"))
(symlink (string-append bootstrap
"/share/web/bootstrap/css/bootstrap.min.css")
(string-append out "/static/bootstrap.min.css"))
(symlink (string-append bootstrap
"/share/web/bootstrap/js/bootstrap.min.js")
(string-append out "/static/bootstrap.min.js"))
(symlink (string-append cytoscape
"/share/genenetwork2/javascript/cytoscape/cytoscape.min.js")
(string-append out "/static/cytoscape.min.js"))
(symlink (string-append jquery
"/share/web/jquery/jquery.slim.min.js")
(string-append out "/static/jquery.slim.min.js"))
;(symlink (string-append js-popper
; "/share/web/popper/popper.min.js")
; (string-append out "/static/popper.min.js"))
)
#t))
(add-after 'install 'wrap-executable
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(path (getenv "PYTHONPATH")))
(wrap-program (string-append out "/server.py")
`("PATH" ":" prefix (,(dirname (which "edirect.pl"))
,(dirname (which "dirname"))
,(dirname (which "grep"))
,(dirname (which "sed"))))
`("PYTHONPATH" ":" prefix (,path))))
#t)))))
(inputs
`(("edirect" ,edirect)
("inetutils" ,inetutils)
("python-bcrypt" ,python-bcrypt)
("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
("python-keras" ,python-keras-for-ratspub)
("python-nltk" ,python-nltk)
("tensorflow" ,tensorflow)))
(native-inputs
`(("bootstrap" ,web-bootstrap)
("cytoscape" ,javascript-cytoscape)
("font-awesome" ,web-font-awesome)
("jquery" ,web-jquery)
;("js-popper" ,js-popper) ; empty output
))
(home-page "http://rats.pub/")
(synopsis "Relationship with Addiction Through Searches of PubMed")
(description
"RatsPub searches PubMed to find sentences that contain the query terms
(i.e., gene symbols) and drug addiction-related keywords. These gene-keyword
relationships are presented as an interactive graph that can efficiently answer
the question \"What do we know about these genes and addiction?\". Data from
@acronym{EBI GWAS, European Bioinformatics Institute Genome-Wide Association
Studies} catalog are also included in the search to better answer this
question.")
(license license:expat)))
;; We want a copy of python-keras without tests.
(define-public python-keras-for-ratspub
(hidden-package
(package
(inherit python-keras)
(arguments
(substitute-keyword-arguments (package-arguments python-keras)
((#:phases phases)
`(modify-phases ,phases
(delete 'check))))))))
|
