From 12a47981f68f8a167bee5b01e405066db03a203d Mon Sep 17 00:00:00 2001
From: Andrey Kislyuk <weaver@gentoo.org>
Date: Sun, 9 Oct 2011 04:01:53 +0000
Subject: [PATCH] Import from Science overlay and rewrite

Package-Manager: portage-2.2.0_alpha45/cvs/Linux x86_64
---
 sci-biology/bedtools/ChangeLog              | 13 +++++++++
 sci-biology/bedtools/Manifest               | 14 +++++++++
 sci-biology/bedtools/bedtools-2.13.3.ebuild | 32 +++++++++++++++++++++
 sci-biology/bedtools/metadata.xml           | 14 +++++++++
 4 files changed, 73 insertions(+)
 create mode 100644 sci-biology/bedtools/ChangeLog
 create mode 100644 sci-biology/bedtools/Manifest
 create mode 100644 sci-biology/bedtools/bedtools-2.13.3.ebuild
 create mode 100644 sci-biology/bedtools/metadata.xml

diff --git a/sci-biology/bedtools/ChangeLog b/sci-biology/bedtools/ChangeLog
new file mode 100644
index 000000000000..dbf5b6263ac9
--- /dev/null
+++ b/sci-biology/bedtools/ChangeLog
@@ -0,0 +1,13 @@
+# ChangeLog for sci-biology/bedtools
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bedtools/ChangeLog,v 1.1 2011/10/09 04:01:53 weaver Exp $
+
+*bedtools-2.13.3 (09 Oct 2011)
+
+  09 Oct 2011; Andrey Kislyuk <weaver@gentoo.org> +bedtools-2.13.3.ebuild,
+  +metadata.xml:
+  Import from Science overlay and rewrite
+
+  24 Jun 2011; Justin Lecher <jlec@gentoo.org> bedtools-2.10.1.ebuild:
+  SOme ebuild cleaning
+
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
new file mode 100644
index 000000000000..4d35840a8783
--- /dev/null
+++ b/sci-biology/bedtools/Manifest
@@ -0,0 +1,14 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+DIST BEDTools.v2.13.3.tar.gz 928205 RMD160 2d4da4fc9f15ac9ba16e733349232822b87a09a9 SHA1 bcd52ba59908c1f98d0c84f4d3fb2e1efb0636d0 SHA256 9c3ec91dfe276005016e002badabf9fa2e12218ed5dbdb30679b5120ed330bbc
+EBUILD bedtools-2.13.3.ebuild 820 RMD160 ee781c0550d4b881bfb4dbdd5154f434076a7379 SHA1 638f696da7369a8f2879edd3d71cb7ba3f0905fc SHA256 b4aa425340ee26d55915ae00b975b0462156a7d8b9446c29418ed1b84adfbc01
+MISC ChangeLog 475 RMD160 7222f0882455a6e09651619a40d60438170a8796 SHA1 7164e706ce82e0c9e7efc61b20e23464b6ba0541 SHA256 0d780fa3070ab58cf2c2244ad90298aa79b61efed7abefe1610e594ad0c49fc2
+MISC metadata.xml 471 RMD160 b3da36bc88c543e8e7589238dc39ea30a0cba58e SHA1 2b966e33142eb4491a33fb385cb70e230884398c SHA256 b845453d89e580a9ef80ba745d64cba010dbba50021aaf6f44bcbf5f28512fa0
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v1.4.11 (GNU/Linux)
+
+iEYEARECAAYFAk6RHLcACgkQ8xSwyhbn2Oa26gCeMC0dKoeW4Sk3FierqSntNkcl
+7QwAni5cd6xyn2mJOFId6jCFKILifVJF
+=ymwO
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/bedtools/bedtools-2.13.3.ebuild b/sci-biology/bedtools/bedtools-2.13.3.ebuild
new file mode 100644
index 000000000000..c635c3de7f27
--- /dev/null
+++ b/sci-biology/bedtools/bedtools-2.13.3.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bedtools/bedtools-2.13.3.ebuild,v 1.1 2011/10/09 04:01:53 weaver Exp $
+
+EAPI=4
+
+inherit flag-o-matic
+
+DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats"
+HOMEPAGE="http://code.google.com/p/bedtools/"
+SRC_URI="http://bedtools.googlecode.com/files/BEDTools.v${PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE=""
+
+S="${WORKDIR}/BEDTools-Version-${PV}"
+
+src_prepare() {
+	filter-ldflags -Wl,--as-needed
+	sed -i -e '1 a SHELL := /bin/bash -e' \
+		-e '/export CXXFLAGS/ d' \
+		-e '/export CXX/ d' \
+		Makefile || die
+}
+
+src_install(){
+	dobin bin/*
+	dodoc README* RELEASE_HISTORY
+	newbin bin/overlap bt_ovelap
+}
diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml
new file mode 100644
index 000000000000..dffdf8b00408
--- /dev/null
+++ b/sci-biology/bedtools/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<maintainer>
+		<email>weaver@gentoo.org</email>
+		<name>Andrey Kislyuk</name>
+	</maintainer>
+	<maintainer>
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<longdescription>BEDTools: a flexible suite of utilities for comparing genomic features.</longdescription>
+</pkgmetadata>
-- 
2.26.2