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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-03-20 16:50:33 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-03-31 17:43:52 +0200 |
| commit | de07c0db4a48cdedc28d7f5b2dcd368f1885e8c9 (patch) | |
| tree | 52902440815400cf22ec364938173caf792e9e38 /gnu/packages/bioinformatics.scm | |
| parent | 8e913213d9d072ddf75c48b8db8f32b46d5a2a3c (diff) | |
| download | patches-de07c0db4a48cdedc28d7f5b2dcd368f1885e8c9.tar patches-de07c0db4a48cdedc28d7f5b2dcd368f1885e8c9.tar.gz | |
gnu: Add vcftools.
* gnu/packages/bioinformatics.scm (vcftools): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 40 |
1 files changed, 40 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 883eb19f6a..651018e0f5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -970,3 +970,43 @@ chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences.") ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed. (license license:gpl3+))) + +(define-public vcftools + (package + (name "vcftools") + (version "0.1.12b") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://sourceforge/vcftools/vcftools_" + version ".tar.gz")) + (sha256 + (base32 + "148al9h7f8g8my2qdnpax51kdd2yjrivlx6frvakf4lz5r8j88wx")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no "check" target + #:make-flags (list + (string-append "PREFIX=" (assoc-ref %outputs "out")) + (string-append "MANDIR=" (assoc-ref %outputs "out") + "/share/man/man1")) + #:phases + (alist-cons-after + 'unpack 'patch-manpage-install + (lambda _ + (substitute* "Makefile" + (("cp \\$\\{PREFIX\\}/cpp/vcftools.1") "cp ./cpp/vcftools.1"))) + (alist-delete 'configure %standard-phases)))) + (inputs + `(("perl" ,perl) + ("zlib" ,zlib))) + (home-page "http://vcftools.sourceforge.net/") + (synopsis "Tools for working with VCF files") + (description + "VCFtools is a program package designed for working with VCF files, such +as those generated by the 1000 Genomes Project. The aim of VCFtools is to +provide easily accessible methods for working with complex genetic variation +data in the form of VCF files.") + ;; The license is declared as LGPLv3 in the README and + ;; at http://vcftools.sourceforge.net/license.html + (license license:lgpl3))) |