Date: Fri, 26 Feb 2016 17:07:59 +0000 (UTC) From: Raphael Kubo da Costa <rakuco@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r409624 - in head/biology: . vcftools Message-ID: <201602261707.u1QH7x7M041595@repo.freebsd.org>
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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 <bacon4000@gmail.com> 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 <bacon4000@gmail.com> +# $FreeBSD$ + +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 <bsd.port.mk> 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
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