From 12cca09b9ad1ee543efaf15e08be3deb844fd741 Mon Sep 17 00:00:00 2001
From: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri, 26 Aug 2016 10:45:50 +0200
Subject: sci-biology/germline: new package

Package-Manager: portage-2.3.0
---
 sci-biology/germline/Manifest              |  1 +
 sci-biology/germline/germline-1.5.1.ebuild | 35 ++++++++++++++++++++++++++++++
 sci-biology/germline/metadata.xml          | 12 ++++++++++
 3 files changed, 48 insertions(+)
 create mode 100644 sci-biology/germline/Manifest
 create mode 100644 sci-biology/germline/germline-1.5.1.ebuild
 create mode 100644 sci-biology/germline/metadata.xml

diff --git a/sci-biology/germline/Manifest b/sci-biology/germline/Manifest
new file mode 100644
index 000000000..3e5e3171f
--- /dev/null
+++ b/sci-biology/germline/Manifest
@@ -0,0 +1 @@
+DIST germline-1-5-1.tar.gz 853549 SHA256 a30b64686a5b3300a7334c98fc09508fd5987c76ab91e149f7c4907d138a7a08 SHA512 d274106a332016f11abaa6aaedf5ca46743647b9074a55e593a3779b965a9cce0607edb06f79e0b380ea81fb0a7112b3fe7518a45c96586dbf4172ed8e820f3e WHIRLPOOL 282352653418eca3f477e629a7eb096d05154ee2b37a642f3ff4858881ff31ffaad82ba77fb14b575774419846863d8fe6e1350d398c70601d6745be534bf552
diff --git a/sci-biology/germline/germline-1.5.1.ebuild b/sci-biology/germline/germline-1.5.1.ebuild
new file mode 100644
index 000000000..e2402fcbe
--- /dev/null
+++ b/sci-biology/germline/germline-1.5.1.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit versionator toolchain-funcs
+
+MY_PV=$(replace_all_version_separators '-')
+
+DESCRIPTION="Find shared segments of Identity by Descent (IBD) between pairs of individuals"
+HOMEPAGE="http://www.cs.columbia.edu/~gusev/germline
+	http://genome.cshlp.org/content/19/2/318.full"
+SRC_URI="http://www.cs.columbia.edu/~gusev/${PN}/${PN}-${MY_PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="dev-libs/boost"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${PN}-${MY_PV}
+
+src_prepare(){
+	sed -e "s/-O3 /${CXXFLAGS} /;s/g++/$(tc-getCXX)/" -i Makefile || die
+	sed -e "s#diff -q -s test/expected.match test/generated.match#diff -q -s test/expected.match test/generated.match || cat test/generated.err#" -i Makefile || die
+	sed -e "s/^all: clean germline bmatch test/all: clean germline bmatch/" -i Makefile || die
+	default
+}
+
+src_install(){
+	dobin germline parse_bmatch
+}
diff --git a/sci-biology/germline/metadata.xml b/sci-biology/germline/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/germline/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>
-- 
cgit v1.2.3-65-gdbad