1 files changed, 44 insertions, 0 deletions
diff --git a/sci-biology/bowtie/bowtie-0.12.8.ebuild b/sci-biology/bowtie/bowtie-0.12.8.ebuild
new file mode 100644
index 000000000000..c26c986ed194
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-0.12.8.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="An ultrafast memory-efficient short read aligner"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86 ~x64-macos"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de)
+# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-gcc-47.patch
+}
+
+src_compile() {
+	unset CFLAGS
+	emake \
+		CC="$(tc-getCC)" \
+		CPP="$(tc-getCXX)" \
+		CXX="$(tc-getCXX)" \
+		EXTRA_FLAGS="${LDFLAGS}" \
+		RELEASE_FLAGS=""
+}
+
+src_install() {
+	dobin bowtie bowtie-*
+	exeinto /usr/share/${PN}/scripts
+	doexe scripts/*
+	newman MANUAL bowtie.1
+	dodoc AUTHORS NEWS TUTORIAL
+}