[gentoo-commits] proj/sci:master commit in: sci-biology/germline/

[Martin Mokrejs]

commit:     12cca09b9ad1ee543efaf15e08be3deb844fd741
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Aug 26 08:45:50 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Aug 26 08:45:50 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=12cca09b

sci-biology/germline: new package

Package-Manager: portage-2.3.0

 sci-biology/germline/germline-1.5.1.ebuild | 35 ++++++++++++++++++++++++++++++
 sci-biology/germline/metadata.xml          | 12 ++++++++++
 2 files changed, 47 insertions(+)

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 0000000..e2402fc
--- /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 0000000..f68a1b6
--- /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@×××××××××××××××.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci-biology@g.o</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>