From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add vcftools. Date: Fri, 20 Mar 2015 16:53:57 +0100 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:33526) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YYzFV-00033h-9E for guix-devel@gnu.org; Fri, 20 Mar 2015 11:54:14 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YYzFQ-0003aO-3o for guix-devel@gnu.org; Fri, 20 Mar 2015 11:54:13 -0400 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]:57085) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YYzFP-0003aD-N5 for guix-devel@gnu.org; Fri, 20 Mar 2015 11:54:08 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id 152482806D2 for ; Fri, 20 Mar 2015 16:54:05 +0100 (CET) Received: from sinope.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 4w1KqNvCQ8Yg for ; Fri, 20 Mar 2015 16:53:59 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Fri, 20 Mar 2015 16:53:59 +0100 (CET) List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: guix-devel --=-=-= Content-Type: text/plain Hi Guix, Attached is a patch to add vcftools. The license of vcftools is declared as LGPLv3.0 here[1] and in the README. ~~ Ricardo --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0001-gnu-Add-vcftools.patch" >From 2f1b826719dbda30bfa63afbb7fd6457981258b3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 Mar 2015 16:50:33 +0100 Subject: [PATCH] gnu: Add vcftools. * gnu/packages/bioinformatics.scm (vcftools): New variable. --- gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5805e42..a6e7e57 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1115,3 +1115,41 @@ combine multiple data representations, algorithm classes, and general purpose tools. This enables both rapid prototyping of data pipelines and extensibility in terms of new algorithms.") (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.") + (license license:lgpl3))) -- 2.1.0 --=-=-=--