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gnu: Add bwa.

* gnu/packages/bioinformatics.scm (bwa): New variable.
This commit is contained in:
Ricardo Wurmus 2015-03-12 12:35:14 +01:00
parent 5762f3062c
commit 9a8336d87b

View file

@ -238,6 +238,53 @@ gapped, local, and paired-end alignment modes.")
(supported-systems '("x86_64-linux"))
(license license:gpl3+)))
(define-public bwa
(package
(name "bwa")
(version "0.7.12")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/bio-bwa/bwa-"
version ".tar.bz2"))
(sha256
(base32
"1330dpqncv0px3pbhjzz1gwgg39kkcv2r9qp2xs0sixf8z8wl7bh"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no "check" target
#:phases
(alist-replace
'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append
(assoc-ref outputs "out") "/bin"))
(doc (string-append
(assoc-ref outputs "out") "/share/doc/bwa"))
(man (string-append
(assoc-ref outputs "out") "/share/man/man1")))
(mkdir-p bin)
(mkdir-p doc)
(mkdir-p man)
(copy-file "bwa" (string-append bin "/bwa"))
(copy-file "README.md" (string-append doc "/README.md"))
(copy-file "bwa.1" (string-append man "/bwa.1"))))
;; no "configure" script
(alist-delete 'configure %standard-phases))))
(inputs `(("zlib" ,zlib)))
(home-page "http://bio-bwa.sourceforge.net/")
(synopsis "Burrows-Wheeler sequence aligner")
(description
"BWA is a software package for mapping low-divergent sequences against a
large reference genome, such as the human genome. It consists of three
algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is
designed for Illumina sequence reads up to 100bp, while the rest two for
longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar
features such as long-read support and split alignment, but BWA-MEM, which is
the latest, is generally recommended for high-quality queries as it is faster
and more accurate. BWA-MEM also has better performance than BWA-backtrack for
70-100bp Illumina reads.")
(license license:gpl3+)))
(define-public clipper
(package
(name "clipper")