From owner-svn-ports-head@freebsd.org Fri Feb 26 17:08:00 2016 Return-Path: Delivered-To: svn-ports-head@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id C3468AB5056; Fri, 26 Feb 2016 17:08:00 +0000 (UTC) (envelope-from rakuco@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id A1893C83; Fri, 26 Feb 2016 17:08:00 +0000 (UTC) (envelope-from rakuco@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id u1QH7xMb041600; Fri, 26 Feb 2016 17:07:59 GMT (envelope-from rakuco@FreeBSD.org) Received: (from rakuco@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id u1QH7x7M041595; Fri, 26 Feb 2016 17:07:59 GMT (envelope-from rakuco@FreeBSD.org) Message-Id: <201602261707.u1QH7x7M041595@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: rakuco set sender to rakuco@FreeBSD.org using -f From: Raphael Kubo da Costa Date: Fri, 26 Feb 2016 17:07:59 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r409624 - in head/biology: . vcftools X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.20 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 26 Feb 2016 17:08:01 -0000 Author: rakuco Date: Fri Feb 26 17:07:59 2016 New Revision: 409624 URL: https://svnweb.freebsd.org/changeset/ports/409624 Log: New port: biology/vcftools. A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project. WWW: https://github.com/vcftools/vcftools PR: 206926 Submitted by: Jason Bacon Added: head/biology/vcftools/ head/biology/vcftools/Makefile (contents, props changed) head/biology/vcftools/distinfo (contents, props changed) head/biology/vcftools/pkg-descr (contents, props changed) head/biology/vcftools/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Fri Feb 26 16:20:17 2016 (r409623) +++ head/biology/Makefile Fri Feb 26 17:07:59 2016 (r409624) @@ -94,6 +94,7 @@ SUBDIR += treepuzzle SUBDIR += treeviewx SUBDIR += ugene + SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt Added: head/biology/vcftools/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vcftools/Makefile Fri Feb 26 17:07:59 2016 (r409624) @@ -0,0 +1,23 @@ +# Created by: Jason Bacon +# $FreeBSD$ + +PORTNAME= vcftools +PORTVERSION= 0.1.14 +DISTVERSIONPREFIX= v +CATEGORIES= biology +DISTNAME= ${PORTNAME}_${PORTVERSION} + +MAINTAINER= bacon4000@gmail.com +COMMENT= Tools for working with VCF genomics files + +LICENSE= LGPL3 + +USES= autoreconf gmake perl5 pkgconfig + +GNU_CONFIGURE= yes +# No zlib.pc on 9.x +CONFIGURE_ENV= ZLIB_CFLAGS=" " ZLIB_LIBS="-lz" + +USE_GITHUB= yes + +.include Added: head/biology/vcftools/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vcftools/distinfo Fri Feb 26 17:07:59 2016 (r409624) @@ -0,0 +1,2 @@ +SHA256 (vcftools_0.1.14_GH0.tar.gz) = ba440584645e9901c1eeb6b769ccd828591f0575c73349072cde3efa77da6fdf +SIZE (vcftools_0.1.14_GH0.tar.gz) = 241228 Added: head/biology/vcftools/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vcftools/pkg-descr Fri Feb 26 17:07:59 2016 (r409624) @@ -0,0 +1,4 @@ +A set of tools written in Perl and C++ for working with VCF files, such as +those generated by the 1000 Genomes Project. + +WWW: https://github.com/vcftools/vcftools Added: head/biology/vcftools/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vcftools/pkg-plist Fri Feb 26 17:07:59 2016 (r409624) @@ -0,0 +1,29 @@ +bin/fill-aa +bin/fill-an-ac +bin/fill-fs +bin/fill-ref-md5 +bin/vcf-annotate +bin/vcf-compare +bin/vcf-concat +bin/vcf-consensus +bin/vcf-contrast +bin/vcf-convert +bin/vcf-fix-newlines +bin/vcf-fix-ploidy +bin/vcf-indel-stats +bin/vcf-isec +bin/vcf-merge +bin/vcf-phased-join +bin/vcf-query +bin/vcf-shuffle-cols +bin/vcf-sort +bin/vcf-stats +bin/vcf-subset +bin/vcf-to-tab +bin/vcf-tstv +bin/vcf-validator +bin/vcftools +%%SITE_PERL%%/FaSlice.pm +%%SITE_PERL%%/Vcf.pm +%%SITE_PERL%%/VcfStats.pm +man/man1/vcftools.1.gz