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
|
(define-module (gn packages gemma)
#: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 ant)
#: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 (gn packages statistics)
#:use-module (gnu packages autotools)
#: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 check)
#:use-module (gnu packages cmake)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpio)
#:use-module (gnu packages curl)
#:use-module (gnu packages documentation)
#:use-module (gnu packages datastructures)
#:use-module (gnu packages check)
#:use-module (gnu packages file)
#:use-module (gnu packages gawk)
#:use-module (gnu packages gcc)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages java)
#:use-module (gnu packages linux)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages node)
#:use-module (gnu packages parallel)
#:use-module (gnu packages pcre)
#: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 ruby)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tbb)
#:use-module (gnu packages textutils)
#:use-module (gnu packages time)
#:use-module (gnu packages tls)
#:use-module (gnu packages vim)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module (gnu packages bootstrap)
#:use-module (gn packages ldc)
#:use-module (gn packages ldc)
#:use-module (gn packages shell)
#:use-module (srfi srfi-1))
(define-public openblas-haswell
(let ((commit "893bd14e924fa72a4ed345a75d64c637f1b1c550"))
(package
(name "openblas-haswell")
(version (string-append "0.2.20-git-" (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/xianyi/OpenBLAS.git")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"0qv03c2yq46p9sajc3a3f56ijfifyv6f4n51a81wc2hihy4ilcap"))))
(build-system gnu-build-system)
(arguments
`(
#:tests? #f ;no "check" target
;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
;; TARGET is specified, OpenBLAS will tune itself to the build host, so
;; we need to disable substitutions.
#:substitutable?
,(let ((system (or (%current-target-system) (%current-system))))
(or (string-prefix? "x86_64" system)
(string-prefix? "i686" system)
(string-prefix? "mips" system)
(string-prefix? "aarch64" system)))
; BINARY=64 NO_WARMUP=0 GEMM_MULTITHREAD_THRESHOLD=4 USE_THREAD=1 NO_AFFINITY=0 NO_LAPACK=0 NUM_THREADS=64
#:make-flags
(list (string-append "PREFIX=" (assoc-ref %outputs "out"))
"SHELL=bash"
"NUM_THREADS=64"
"BINARY=64"
"NO_WARMUP=0"
"GEMM_MULTITHREAD_THRESHOLD=4"
"USE_THREAD=1"
"NO_AFFINITY=0"
"NO_LAPACK=0" ; use OpenBlas LAPACK
"COMMON_PROF=0" ; disable profiling
"DEBUG=0"
;; Build the library for all supported CPUs. This allows
;; switching CPU targets at runtime with the environment variable
;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
;; Unfortunately, this is not supported on non-x86 architectures,
;; where it leads to failed builds.
,@(let ((system (or (%current-target-system) (%current-system))))
(cond
; ((or (string-prefix? "x86_64" system)
; (string-prefix? "i686" system))
((string-prefix? "x86_64" system)
'("TARGET=HASWELL"))
;; On MIPS we force the "SICORTEX" TARGET, as for the other
;; two available MIPS targets special extended instructions
;; for Loongson cores are used.
((string-prefix? "mips" system)
'("TARGET=SICORTEX"))
;; On aarch64 force the generic 'armv8-a' target
((string-prefix? "aarch64" system)
'("TARGET=ARMV8"))
(else '()))))
;; no configure script
#:phases (alist-delete 'configure %standard-phases)))
(inputs
`(("gfortran" ,gfortran)
("gfortran:lib" ,gfortran "lib")))
(native-inputs
`(("cunit" ,cunit)
("perl" ,perl)))
(home-page "http://www.openblas.net/")
(synopsis "Platform optimized BLAS library based on GotoBLAS")
(description
"OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
(license license:bsd-3))))
(define-public gsl1 ; supporting older GSL tests
(package
(name "gsl1")
(version "1.16")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/gsl/gsl-"
version ".tar.gz"))
(sha256
(base32
"0lrgipi0z6559jqh82yx8n4xgnxkhzj46v96dl77hahdp58jzg3k"))
))
(build-system gnu-build-system)
(home-page "https://www.gnu.org/software/gsl/")
(synopsis "Numerical library for C and C++")
(description
"The GNU Scientific Library is a library for numerical analysis in C
and C++. It includes a wide range of mathematical routines, with over 1000
functions in total. Subject areas covered by the library include:
differential equations, linear algebra, Fast Fourier Transforms and random
numbers.")
(license license:gpl3+)))
(define-public gemma-git-gn2 ; guix candidate
(let ((commit "c760aa09c2aa91ca6270b5f898c27e9aed376a73"))
(package
(name "gemma-git-gn2")
(version (string-append "0.97-" (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/genenetwork/GEMMA")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"0s61w8av70kqvkb00znrqnr59axygh9gnlxar8rfyasr5g6xvl8w"))))
(inputs `(
("gfortran:lib" ,gfortran "lib")
("gsl" ,gsl)
("eigen" ,eigen)
("shunit2" ,shunit2)
; ("lapack" ,lapack) - included in openblas-haswell
("openblas" ,openblas-haswell)
("zlib" ,zlib)
))
(native-inputs ; for running tests
`(("perl" ,perl)
("which" ,which)
))
(build-system gnu-build-system)
(arguments
`(#:make-flags
(list
(string-append "EIGEN_INCLUDE_PATH="
(assoc-ref %build-inputs "eigen")
"/include/eigen3/")
)
#:phases
; "/include/eigen3/"
(modify-phases %standard-phases
(delete 'configure)
(add-before 'build 'bin-mkdir
(lambda _
(mkdir-p "bin")
))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(install-file "bin/gemma" (string-append out "/bin"))))))
; #:tests? #f
#:parallel-tests? #f))
(home-page "http://www.xzlab.org/software.html")
(synopsis "Tool for genome-wide efficient mixed model association")
(description "GEMMA is the software implementing the Genome-wide
Efficient Mixed Model Association algorithm for a standard linear
mixed model and some of its close relatives for genome-wide
association studies (GWAS).")
(license license:gpl3))))
(define-public gemma-gn2
(package
(name "gemma")
(version "0.96")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/xiangzhou/GEMMA/archive/v"
version ".tar.gz"))
(sha256
(base32
"055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222"))))
(inputs `(("gsl" ,gsl)
("lapack" ,lapack)
("zlib" ,zlib)))
(build-system gnu-build-system)
(arguments
`(#:make-flags '("FORCE_DYNAMIC=1")
#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-before 'build 'bin-mkdir
(lambda _
(mkdir-p "bin")
))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(install-file "bin/gemma" (string-append out "/bin"))))))
#:tests? #f)) ; no tests included
(home-page "")
(synopsis "Tool for genome-wide efficient mixed model association")
(description "GEMMA is software implementing the Genome-wide
Efficient Mixed Model Association algorithm for a standard linear
mixed model and some of its close relatives for genome-wide
association studies (GWAS).")
(license license:gpl3)))
(define-public gemma-wrapper
(package
(name "gemma-wrapper")
(version "0.92.2")
(source
(origin
(method url-fetch)
(uri (rubygems-uri "bio-gemma-wrapper" version))
(sha256
(base32
"08apz0imsxzwhzv2iicq2g5zx1iq1vlfrhk7khsfaydshbq5g741"))))
(build-system ruby-build-system)
(inputs `(("gemma-git-gn2" ,gemma-git-gn2)))
(arguments
`(#:tests? #f
#:phases
(modify-phases %standard-phases
(add-before
'build 'set-gemma-path
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(substitute* "bin/gemma-wrapper"
; (("gemma_command = ENV['GEMMA_COMMAND']")
(("gemma_command = ENV.*")
(string-append "gemma_command = '" (which "gemma") "'")))
))))))
(synopsis
"Gemma wrapper for LOCO and caching")
(description "Gemma wrapper")
(home-page "https://rubygems.org/gems/bio-gemma-wrapper")
(license license:gpl3)))
|
