gnu: Add vcftools.
* gnu/packages/bioinformatics.scm (vcftools): New variable.
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@ -970,3 +970,43 @@ chimeric (fusion) transcripts, and is also capable of mapping full-length RNA
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sequences.")
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;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
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(license license:gpl3+)))
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(define-public vcftools
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(package
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(name "vcftools")
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(version "0.1.12b")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"mirror://sourceforge/vcftools/vcftools_"
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version ".tar.gz"))
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(sha256
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(base32
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"148al9h7f8g8my2qdnpax51kdd2yjrivlx6frvakf4lz5r8j88wx"))))
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #f ; no "check" target
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#:make-flags (list
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(string-append "PREFIX=" (assoc-ref %outputs "out"))
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(string-append "MANDIR=" (assoc-ref %outputs "out")
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"/share/man/man1"))
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#:phases
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(alist-cons-after
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'unpack 'patch-manpage-install
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(lambda _
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(substitute* "Makefile"
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(("cp \\$\\{PREFIX\\}/cpp/vcftools.1") "cp ./cpp/vcftools.1")))
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(alist-delete 'configure %standard-phases))))
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(inputs
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`(("perl" ,perl)
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("zlib" ,zlib)))
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(home-page "http://vcftools.sourceforge.net/")
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(synopsis "Tools for working with VCF files")
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(description
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"VCFtools is a program package designed for working with VCF files, such
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as those generated by the 1000 Genomes Project. The aim of VCFtools is to
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provide easily accessible methods for working with complex genetic variation
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data in the form of VCF files.")
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;; The license is declared as LGPLv3 in the README and
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;; at http://vcftools.sourceforge.net/license.html
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(license license:lgpl3)))
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