From a58f8020918ebfc342dd2c596e4c25441bd665db Mon Sep 17 00:00:00 2001
From: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri, 26 Aug 2016 10:40:58 +0200
Subject: sci-biology/vcflib: new package, works though is not ideal

Package-Manager: portage-2.3.0
---
 sci-biology/vcflib/metadata.xml       | 12 ++++++++++
 sci-biology/vcflib/vcflib-9999.ebuild | 43 +++++++++++++++++++++++++++++++++++
 2 files changed, 55 insertions(+)
 create mode 100644 sci-biology/vcflib/metadata.xml
 create mode 100644 sci-biology/vcflib/vcflib-9999.ebuild

diff --git a/sci-biology/vcflib/metadata.xml b/sci-biology/vcflib/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/vcflib/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/vcflib/vcflib-9999.ebuild b/sci-biology/vcflib/vcflib-9999.ebuild
new file mode 100644
index 000000000..5a03fe42b
--- /dev/null
+++ b/sci-biology/vcflib/vcflib-9999.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit git-r3 toolchain-funcs
+
+DESCRIPTION="VCF/BED utils, Genotype Phenotype Association Toolkit (GPAT++)"
+HOMEPAGE="https://github.com/vcflib/vcflib"
+EGIT_REPO_URI="https://github.com/vcflib/vcflib.git"
+
+# vcflib is incorporated into several projects, such as freebayes
+
+LICENSE="MIT-with-advertising"
+SLOT="0"
+KEYWORDS=""
+IUSE="mpi"
+
+DEPEND="mpi? ( sys-cluster/openmpi )"
+RDEPEND="${DEPEND}"
+# contains bundled sci-biology/htslib ?
+# see also ./include for possible traces of other bundled sw
+
+src_prepare(){
+	default
+	sed -e "s/^CXX = g++/CXX = $(tc-getCXX)/" -i Makefile || die
+	sed -e "s/^CXXFLAGS = -O3/CXXFLAGS = ${CXXFLAGS}/" -i Makefile || die
+}
+
+src_compile(){
+	if use mpi ; then
+		emake openmp
+	else
+		emake
+	fi
+}
+
+src_install(){
+	dobin bin/*
+	dolib lib/* # install libvcflib.a
+	dodoc README.md
+}
-- 
cgit v1.2.3-65-gdbad