Import /home/bacon/Pkgsrc/pkgsrc-2016Q1/wip/ vcftools vcftools-0.1.14 as wip/vcftools.

[Jason Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed May 11 13:22:52 2016 -0500
Changeset:	72330bae7212b790a962d5754b7f8d9ac00b275a

Added Files:
	vcftools/DESCR
	vcftools/Makefile
	vcftools/PLIST
	vcftools/TODO
	vcftools/buildlink3.mk
	vcftools/distinfo

Log Message:
Import /home/bacon/Pkgsrc/pkgsrc-2016Q1/wip/vcftools
vcftools-0.1.14 as wip/vcftools.

A set of tools written in Perl and C++ for working with VCF files, such as
those generated by the 1000 Genomes Project.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=72330bae7212b790a962d5754b7f8d9ac00b275a

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 vcftools/DESCR         |  2 ++
 vcftools/Makefile      | 36 ++++++++++++++++++++++++++++++++++++
 vcftools/PLIST         | 30 ++++++++++++++++++++++++++++++
 vcftools/TODO          |  1 +
 vcftools/buildlink3.mk | 30 ++++++++++++++++++++++++++++++
 vcftools/distinfo      |  6 ++++++
 6 files changed, 105 insertions(+)

diffs:
diff --git a/vcftools/DESCR b/vcftools/DESCR
new file mode 100644
index 0000000..3bb9368
--- /dev/null
+++ b/vcftools/DESCR
@@ -0,0 +1,2 @@
+A set of tools written in Perl and C++ for working with VCF files, such as
+those generated by the 1000 Genomes Project.
diff --git a/vcftools/Makefile b/vcftools/Makefile
new file mode 100644
index 0000000..2eb5859
--- /dev/null
+++ b/vcftools/Makefile
@@ -0,0 +1,36 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Wed May 11 13:04:07 CDT 2016               #
+###########################################################
+
+DISTNAME=	vcftools_${PORTVERSION}
+PKGNAME=	vcftools-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=vcftools/}
+GITHUB_PROJECT=	vcftools
+GITHUB_TAG=	v${PORTVERSION}
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+HOMEPAGE=	https://github.com/vcftools/vcftools
+COMMENT=	Tools for working with VCF genomics files
+LICENSE=	gnu-lgpl-v3
+
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	autoconf automake autoreconf gmake perl pkg-config
+GNU_CONFIGURE=	yes
+REPLACE_PERL=	src/perl/*
+
+# No zlib.pc on FreeBSD 9.x
+CONFIGURE_ENV=	ZLIB_CFLAGS=" " ZLIB_LIBS="-lz"
+
+FETCH_USING=	curl
+
+PORTVERSION=	0.1.14
+
+pre-configure:
+	cd ${WRKSRC} && autoreconf -if
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/vcftools/PLIST b/vcftools/PLIST
new file mode 100644
index 0000000..0dce911
--- /dev/null
+++ b/vcftools/PLIST
@@ -0,0 +1,30 @@
+@comment $NetBSD$
+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/vcftools
+bin/vcf-to-tab
+bin/vcf-tstv
+bin/vcf-validator
+lib/perl5/site_perl/5.22.0/FaSlice.pm
+lib/perl5/site_perl/5.22.0/Vcf.pm
+lib/perl5/site_perl/5.22.0/VcfStats.pm
+man/man1/vcftools.1
diff --git a/vcftools/TODO b/vcftools/TODO
new file mode 100644
index 0000000..b687356
--- /dev/null
+++ b/vcftools/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/vcftools/buildlink3.mk b/vcftools/buildlink3.mk
new file mode 100644
index 0000000..ebcdb13
--- /dev/null
+++ b/vcftools/buildlink3.mk
@@ -0,0 +1,30 @@
+# $NetBSD$
+# XXX
+# XXX This file was created automatically using createbuildlink-3.17.
+# XXX After this file has been verified as correct, the comment lines
+# XXX beginning with "XXX" should be removed.  Please do not commit
+# XXX unverified buildlink3.mk files.
+# XXX
+# XXX Packages that only install static libraries or headers should
+# XXX include the following line:
+# XXX
+# XXX	BUILDLINK_DEPMETHOD.vcftools?=	build
+
+BUILDLINK_TREE+=	vcftools
+
+.if !defined(VCFTOOLS_BUILDLINK3_MK)
+VCFTOOLS_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.vcftools+=	vcftools>=0.1.14
+BUILDLINK_PKGSRCDIR.vcftools?=	../../wip/vcftools
+
+# XXX
+# XXX Uncomment and keep only the buildlink3 lines below which are directly
+# XXX needed for dependencies to compile, link, and run.  If this package
+# XXX provides a wrappered API or otherwise does not expose the APIs of the
+# XXX buildlink3 lines below to dependencies, remove them.
+# XXX
+#.include "../../devel/zlib/buildlink3.mk"
+.endif	# VCFTOOLS_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-vcftools
diff --git a/vcftools/distinfo b/vcftools/distinfo
new file mode 100644
index 0000000..b946f46
--- /dev/null
+++ b/vcftools/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (vcftools_0.1.14.tar.gz) = e816a7f11297646b4b8b9682516d635b90736c75
+RMD160 (vcftools_0.1.14.tar.gz) = b6839448323a6401ff6233394c4a692ff14c7cba
+SHA512 (vcftools_0.1.14.tar.gz) = 1cb3c02dca2785d3405f2e532cc13fa9ea03138ef3ac23171313eb740975062b073f8a57c5826afa4355140a8388edd9f24b46ad8bba8b75b1e04368537dd435
+Size (vcftools_0.1.14.tar.gz) = 241228 bytes