From d75a33f9120a279b8d70c76ea85a078939dcf0b3 Mon Sep 17 00:00:00 2001
From: Andrey Kislyuk <weaver@gentoo.org>
Date: Mon, 21 Jan 2013 06:15:22 +0000
Subject: Version bump

(Portage version: 2.2.0_alpha134/cvs/Linux x86_64)
---
 sci-biology/bwa/ChangeLog        |  9 +++++++--
 sci-biology/bwa/bwa-0.6.2.ebuild | 35 +++++++++++++++++++++++++++++++++++
 2 files changed, 42 insertions(+), 2 deletions(-)
 create mode 100644 sci-biology/bwa/bwa-0.6.2.ebuild

(limited to 'sci-biology/bwa')

diff --git a/sci-biology/bwa/ChangeLog b/sci-biology/bwa/ChangeLog
index fe95fdbb5394..a227c899b47d 100644
--- a/sci-biology/bwa/ChangeLog
+++ b/sci-biology/bwa/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/bwa
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bwa/ChangeLog,v 1.11 2011/11/30 08:44:21 weaver Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bwa/ChangeLog,v 1.12 2013/01/21 06:15:22 weaver Exp $
+
+*bwa-0.6.2 (21 Jan 2013)
+
+  21 Jan 2013; Andrey Kislyuk <weaver@gentoo.org> +bwa-0.6.2.ebuild:
+  Version bump
 
 *bwa-0.6.1 (30 Nov 2011)
 
diff --git a/sci-biology/bwa/bwa-0.6.2.ebuild b/sci-biology/bwa/bwa-0.6.2.ebuild
new file mode 100644
index 000000000000..9430a23b2e0d
--- /dev/null
+++ b/sci-biology/bwa/bwa-0.6.2.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bwa/bwa-0.6.2.ebuild,v 1.1 2013/01/21 06:15:22 weaver Exp $
+
+EAPI=2
+
+inherit flag-o-matic toolchain-funcs
+
+DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner"
+HOMEPAGE="http://bio-bwa.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+src_prepare() {
+	sed -e "s/\$(CC) \$(CFLAGS)/\$(CC) \$(LDFLAGS) \$(CFLAGS)/" \
+		-i "${S}"/Makefile || die #336348
+	append-flags -pthread
+}
+
+src_compile() {
+	emake -e CC="$(tc-getCC)" || die
+}
+
+src_install() {
+	dobin bwa || die
+	doman bwa.1 || die
+	exeinto /usr/share/${PN}
+	doexe solid2fastq.pl || die
+	doexe qualfa2fq.pl || die
+	dodoc ChangeLog NEWS || die
+}
-- 
cgit v1.2.3-65-gdbad