1 files changed, 35 insertions, 0 deletions
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
+}