From de07c0db4a48cdedc28d7f5b2dcd368f1885e8c9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 20 Mar 2015 16:50:33 +0100
Subject: gnu: Add vcftools.

* gnu/packages/bioinformatics.scm (vcftools): New variable.
---
 gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

(limited to 'gnu')

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)))
-- 
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