svn commit: r409624 - in head/biology: . vcftools

[Raphael Kubo da Costa]

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 at 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 at gmail.com>
+# $FreeBSD$
+
+PORTNAME=	vcftools
+PORTVERSION=	0.1.14
+DISTVERSIONPREFIX=	v
+CATEGORIES=	biology
+DISTNAME=	${PORTNAME}_${PORTVERSION}
+
+MAINTAINER=	bacon4000 at 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