gnu: Add bcftools.

* gnu/packages/bioinformatics.scm (bcftools): New variable.
This commit is contained in:
Marius Bakke 2016-09-22 13:47:53 +01:00 committed by Ben Woodcroft
parent e301bfc886
commit bdc7be59eb
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@ -265,6 +265,64 @@ (define-public bamtools
BAM files.")
(license license:expat)))
(define-public bcftools
(package
(name "bcftools")
(version "1.3.1")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/samtools/bcftools/releases/download/"
version "/bcftools-" version ".tar.bz2"))
(sha256
(base32
"095ry68vmz9q5s1scjsa698dhgyvgw5aicz24c19iwfbai07mhqj"))
(modules '((guix build utils)))
(snippet
;; Delete bundled htslib.
'(delete-file-recursively "htslib-1.3.1"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
#:make-flags
(list
"USE_GPL=1"
(string-append "prefix=" (assoc-ref %outputs "out"))
(string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include")
(string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.a")
(string-append "BGZIP=" (assoc-ref %build-inputs "htslib") "/bin/bgzip")
(string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix"))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-Makefile
(lambda _
(substitute* "Makefile"
;; Do not attempt to build htslib.
(("^include \\$\\(HTSDIR\\)/htslib\\.mk") "")
;; Link against GSL cblas.
(("-lcblas") "-lgslcblas"))
#t))
(delete 'configure)
(add-before 'check 'patch-tests
(lambda _
(substitute* "test/test.pl"
(("/bin/bash") (which "bash")))
#t)))))
(native-inputs
`(("htslib" ,htslib)
("perl" ,perl)))
(inputs
`(("gsl" ,gsl)
("zlib" ,zlib)))
(home-page "https://samtools.github.io/bcftools/")
(synopsis "Utilities for variant calling and manipulating VCFs and BCFs")
(description
"BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF. All commands work
transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1.
(license (list license:gpl3+ license:expat))))
(define-public bedops
(package
(name "bedops")