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
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
|
;; Bioinformatics module
(define-module (gn packages genenetwork)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix utils)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix build-system gnu)
#:use-module (guix build-system cmake)
#:use-module (guix build-system perl)
#:use-module (guix build-system python)
;; #:use-module (guix build-system ruby)
#:use-module (guix build-system r)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
#:use-module (gnu packages databases)
#:use-module (gnu packages cpio)
#:use-module (gnu packages file)
#:use-module (gnu packages gcc)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages java)
#:use-module (gnu packages linux)
#:use-module (gnu packages ldc)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tbb)
#:use-module (gnu packages textutils)
#:use-module (gnu packages vim)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module (gnu packages zip)
#:use-module (gnu packages bootstrap)
#:use-module (gn packages bioinformatics)
#:use-module (gn packages python)
#:use-module (gn packages statistics)
#:use-module (srfi srfi-1))
(define-public my-deploy
(package
(name "my-deploy")
(version "0.0.1")
(source #f)
(build-system trivial-build-system)
(arguments
`(#:guile ,%bootstrap-guile
#:modules ((guix build utils))
#:builder
(let* ((out (assoc-ref %outputs "out"))
(bash (assoc-ref %build-inputs "bash"))
(foo (string-append out "/foo")))
(begin
(use-modules (guix build utils))
(mkdir out)
(call-with-output-file foo
(lambda (p)
(format p
"#!~a~%echo \"${GUIX_FOO} ${GUIX_BAR}\"~%"
bash)))
(chmod foo #o777)
;; wrap-program uses `which' to find bash for the wrapper
;; shebang, but it can't know about the bootstrap bash in
;; the store, since it's not named "bash". Help it out a
;; bit by providing a symlink it this package's output.
(symlink bash (string-append out "/bash"))
(setenv "PATH" out)
(wrap-program foo `("GUIX_FOO" prefix ("hello")))
(wrap-program foo `("GUIX_BAR" prefix ("world")))
#t))))
(inputs `(("bash" ,(search-bootstrap-binary "bash"
(%current-system)))))
(home-page #f)
(synopsis #f)
(description #f)
(license #f)))
(define-public genenetwork1
(let ((commit "d622c803b"))
(package
(name "genenetwork1")
(version (string-append "1.0-" commit ))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/genenetwork/genenetwork.git")
;; (url "https://github.com/pjotrp/genenetwork.git")
(commit commit)))
(file-name (string-append name "-" commit))
(sha256
(base32
"14fzfcm4vl20mlhxjslfa01i1nmxpk8lbxmfvpq6dyfc22ir62py"))))
(propagated-inputs `(
("python" ,python-2) ;; probably superfluous
("r" ,r)
))
(inputs `(
;; http://spring211.uthsc.edu/gn/thirdparty.tbz
;; graphviz-2.22.2 htmlgen json numarray-1.5.2 piddle PIL pp-1.5.7 pyx pyXLWriter svg
("mysql" ,mysql)
("nginx" ,nginx)
("graphviz" ,graphviz)
; ("python2-jinja2" ,python2-jinja2)
; ("python2-sqlalchemy" ,python2-sqlalchemy)
; ("python2-setuptools" ,python2-setuptools)
; ("python2-scipy" ,python2-scipy)
;; looks like python-numarray is not needed
; ("python2-numpy" ,python2-numpy)
; ("python2-pandas" ,python2-pandas)
; ("python2-passlib" ,python2-passlib)
; ("python2-redis" ,python2-redis)
; ("python2-requests" ,python2-requests)
; ("python2-simplejson" ,python2-simplejson)
; ("python2-pyyaml" ,python2-pyyaml)
;; python-yolk is not needed
("python2-pillow" ,python2-pillow)
("python2-numarray" ,python2-numarray)
("plink" ,plink) ;; gn1
; ("r-qtl" ,r-qtl)
))
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:tests? #f)) ; no 'setup.py test'
(home-page "http://genenetwork.org/")
(synopsis "Full genenetwork services")
(description "Genenetwork installation sumo.")
(license license:agpl3+))))
(define-public genenetwork2
(let ((commit "a8fcff44d3bd768d02e7ed0c80b84d2516bdad2a"))
(package
(name "genenetwork2")
(version (string-append "2.0-" (string-take commit 7) ))
(source (origin
(method git-fetch)
(uri (git-reference
;; (url "https://github.com/genenetwork/genenetwork2.git")
(url "https://github.com/genenetwork/genenetwork2_diet.git")
(commit commit)))
(file-name (string-append name "-" (string-take commit 7)))
(sha256
(base32
"1zs6jgrpwzxmfjz03whnaw8q6h8f53mycl440p058gfn8x7pd618"))))
(propagated-inputs `( ;; propagated for development purposes
("python" ,python-2) ;; probably superfluous
("r" ,r)
("r-wgcna" ,r-wgcna)
("r-qtl" ,r-qtl)
("redis" ,redis)
("mysql" ,mysql)
("gemma" ,gemma-git)
("genenetwork2-files-small" ,genenetwork2-files-small)
("pylmm-gn2" ,pylmm-gn2)
;; ("plink2" ,plink-ng) disabled - FIXME
("nginx" ,nginx)
("python2-flask" ,python2-flask)
("python2-htmlgen-gn" ,python2-htmlgen-gn)
("python2-jinja2" ,python2-jinja2)
("python2-sqlalchemy" ,python2-sqlalchemy)
("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy)
("python2-setuptools" ,python2-setuptools)
("python2-scipy" ,python2-scipy)
("python2-mysqlclient" ,python2-mysqlclient)
("python2-numarray" ,python2-numarray)
("python2-numpy" ,python2-numpy)
("python2-pandas" ,python2-pandas)
("python2-parallel" ,python2-parallel)
("python2-passlib" ,python2-passlib)
("python2-piddle-gn" ,python2-piddle-gn)
("python2-redis" ,python2-redis)
("python2-pillow" ,python2-pillow)
("python2-requests" ,python2-requests)
("python2-rpy2" ,python2-rpy2)
("python2-scipy" ,python2-scipy)
("python2-simplejson" ,python2-simplejson)
("python2-pyyaml" ,python2-pyyaml)
("python2-xlsxwriter" ,python2-xlsxwriter)
("qtlreaper" ,qtlreaper)
))
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:phases
(modify-phases %standard-phases
(add-before 'install 'fix-paths
(lambda* (#:key inputs #:allow-other-keys)
(let* (
(datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" ))
(pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis"))
;; (plink2cmd (string-append (assoc-ref inputs "plink2") "/bin/plink2"))
(gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))
)
(substitute* '("etc/default_settings.py")
(("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" ))
(("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" ))
;; (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
(("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" ))
)
))))
#:tests? #f)) ; no 'setup.py test'
(home-page "http://genenetwork.org/")
(synopsis "Full genenetwork services")
(description "Genenetwork installation sumo.")
(license license:agpl3+))))
;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip
;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x
(define-public genenetwork2-files-small
(let ((pfff "xx"))
(package
(name "genenetwork2-files-small")
(version "1.0")
(source
(origin
(method url-fetch)
(uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4")
(file-name (string-append name "-" pfff))
(sha256
(base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj"))))
(build-system trivial-build-system)
(native-inputs `(("lz4" ,lz4)
("tar" ,tar)
("source" ,source)))
(arguments
`(#:modules ((guix build utils))
#:builder
(let* ((out (assoc-ref %outputs "out"))
(name "gn2_data_s")
(tarfn (string-append name ".tar"))
(targetdir (string-append out "/share/genenetwork2/"))
)
(begin
(use-modules (guix build utils))
(let ((source (assoc-ref %build-inputs "source"))
(lz4unpack (string-append (assoc-ref %build-inputs "lz4") "/bin/lz4"))
(tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar"))
)
(and
(zero? (system* lz4unpack source "-d" tarfn))
(zero? (system* tar "xf" tarfn))
(mkdir-p targetdir)
(copy-recursively name targetdir)
))))))
(home-page "http://genenetwork.org/")
(synopsis "Small file archive to run on genenetwork")
(description "Genenetwork genotype and mapping files.")
(license license:agpl3+))))
(define-public genenetwork2-database-small
(let ((md5 "93e745e9c"))
(package
(name "genenetwork2-database-small")
(version "1.0")
(source
(origin
(method url-fetch)
(uri "http://files.genenetwork.org/raw_database/db_webqtl_s.zip")
(file-name (string-append name "-" md5))
(sha256
(base32 "0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x"))))
(build-system trivial-build-system)
(native-inputs `(("unzip" ,unzip)
("source" ,source)))
(arguments
`(#:modules ((guix build utils))
#:builder (begin
(use-modules (guix build utils))
(let ((source (assoc-ref %build-inputs "source"))
(unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip"))
)
(and (mkdir "db")
(zero? (system* unzip source "-d" "db"))
(chdir "db"))))))
(home-page "http://genenetwork.org/")
(synopsis "Small database to run on genenetwork")
(description "Genenetwork installation + database.")
(license license:agpl3+))))
|
