From cec254823f198e90b0c51750704aab40e9e0c64c Mon Sep 17 00:00:00 2001
From: David Seifert <soap@gentoo.org>
Date: Sun, 25 Sep 2016 11:44:52 +0200
Subject: sci-biology/vcftools: remove, in main tree

---
 sci-biology/vcftools/Manifest               |  1 -
 sci-biology/vcftools/metadata.xml           | 11 ------
 sci-biology/vcftools/vcftools-0.1.14.ebuild | 55 -----------------------------
 3 files changed, 67 deletions(-)
 delete mode 100644 sci-biology/vcftools/Manifest
 delete mode 100644 sci-biology/vcftools/metadata.xml
 delete mode 100644 sci-biology/vcftools/vcftools-0.1.14.ebuild

diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest
deleted file mode 100644
index 0fa99d3bb..000000000
--- a/sci-biology/vcftools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST vcftools-vcftools-v0.1.14-14-g2543f81.tar.gz 241876 SHA256 9d9eece6e766ec75162d1edc0e95df1710896f4230531cbc92826f53505ec6e5 SHA512 29735d6ab7c1f91c155bc86fdab462cd590fbf296d1f3ad99a99e2a4882a0f30c50cb222d875fbc2d7cf480244385c29184096f083d34cd0ef9b6f93737ef6a9 WHIRLPOOL f3a7ccc443830466157a2168e12fdc5b061456c316b2f0891ab8c9ed4edc96654d39389a5268ecc051092154e20f83efa3de357fa6aaa823fc8b69819d2676da
diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml
deleted file mode 100644
index 77f6f92e0..000000000
--- a/sci-biology/vcftools/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">vcftools</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/vcftools/vcftools-0.1.14.ebuild b/sci-biology/vcftools/vcftools-0.1.14.ebuild
deleted file mode 100644
index 0e792f8b2..000000000
--- a/sci-biology/vcftools/vcftools-0.1.14.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs autotools
-
-MY_P="${PN}_${PV}"
-
-DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
-HOMEPAGE="https://vcftools.github.io
-	http://vcftools.sourceforge.net"
-SRC_URI="https://github.com/vcftools/vcftools/archive/vcftools-vcftools-v0.1.14-14-g2543f81.tar.gz"
-#SRC_URI="https://codeload.github.com/vcftools/vcftools/legacy.tar.gz/master -> ${P}.tar.gz"
-#SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE="lapack"
-
-RDEPEND="lapack? ( virtual/lapack )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}"/vcftools-vcftools-2543f81
-#S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	# epatch "${FILESDIR}"/${P}-buildsystem.patch
-	tc-export CXX PKG_CONFIG
-	eautoreconf
-}
-
-src_configure(){
-	econf --enable-pca # --with-pmdir=DIR   install Perl modules in DIR
-}
-
-#src_compile() {
-#	local myconf
-#	use lapack && myconf="VCFTOOLS_PCA=1"
-#	emake -C cpp ${myconf}
-#}
-
-src_install(){
-	perl_set_version
-	dobin src/cpp/"${PN}"
-	doman src/cpp/"${PN}".1
-	insinto "${VENDOR_LIB}"
-	doins src/perl/*.pm
-	dobin src/perl/{fill,vcf}-*
-	dodoc README.md
-}
-- 
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