blob: e64ff983286eabd1846bb75477b5b33c90aefa26 (
plain)
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
|
;; To use this file to build HEAD of gemma:
;;
;; guix build -f guix.scm
;;
;; To get a development container (e.g., run in emacs shell).
;;
;; guix shell -C -f guix.scm
(use-modules
((guix licenses) #:prefix license:)
(guix gexp)
(guix packages)
(guix git-download)
(guix build-system gnu)
(gnu packages algebra)
(gnu packages base)
(gnu packages compression)
(gnu packages bioinformatics)
(gnu packages build-tools)
(gnu packages check)
(gnu packages curl)
(gnu packages gdb)
(gnu packages llvm)
(gnu packages maths)
(gnu packages ninja)
(gnu packages parallel)
(gnu packages perl)
;; (gnu packages perl6)
(gnu packages ruby)
(gnu packages pkg-config)
;; (gnu packages shell) ;; for shunit2
(srfi srfi-1)
(ice-9 popen)
(ice-9 rdelim))
(define %source-dir (dirname (current-filename)))
(define %git-commit
(read-string (open-pipe "git show HEAD | head -1 | cut -d ' ' -f 2" OPEN_READ)))
(define %gemma-version
(read-string (open-pipe "cat VERSION" OPEN_READ)))
(define-public gemma-git
(package
(name "gemma-git")
(version (git-version "0.98.5" "HEAD" %git-commit))
(source (local-file %source-dir #:recursive? #t))
(build-system gnu-build-system)
(inputs `(
("catch" ,catch2)
("gdb" ,gdb)
("gsl" ,gsl)
;; ("shunit2" ,shunit2) ;; comes with gemma
("openblas" ,openblas)
("ruby" ,ruby) ;; for testing
("zlib:static" ,zlib "static")
("zlib" ,zlib)
))
(native-inputs ; for running tests
`(("perl" ,perl)
("which" ,which)
))
(arguments
`(#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'validate-runpath)
(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? #t
#:parallel-tests? #f))
(home-page "https://github.com/genetics-statistics")
(synopsis "Tool for genome-wide efficient mixed model association")
(description "Genome-wide Efficient Mixed Model Association (GEMMA)
provides a standard linear mixed model resolver with application in
genome-wide association studies (GWAS).")
(license license:gpl3)))
gemma-git
|
