1 files changed, 61 insertions, 0 deletions
diff --git a/sci-biology/bowtie/bowtie-2.1.0.ebuild b/sci-biology/bowtie/bowtie-2.1.0.ebuild
new file mode 100644
index 000000000..c2c502442
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-2.1.0.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+DESCRIPTION="An ultrafast memory-efficient short read aligner"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-source.zip"
+
+LICENSE="GPL-3"
+SLOT="2"
+IUSE="sse2 examples"
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="dev-lang/perl"
+DEPEND="${CDEPEND} \
+		app-arch/unzip"
+RDEPEND="${CDEPEND}"
+
+S="${WORKDIR}/${PN}2-${PV}"
+
+pkg_pretend() {
+	if ! use sse2 ; then
+		ebegin
+		eerror "bowtie2 requires sse2 support. Please make sure your system supports"
+		eerror "sse2 and enable the sse2 use flag."
+		eend
+		die
+	fi
+}
+
+src_prepare() {
+	epatch "${FILESDIR}/${P}-buildsystem.patch"
+}
+
+src_compile() {
+	use sse2 && append-cxxflags -msse2
+	emake \
+		CC="$(tc-getCC)" \
+		CPP="$(tc-getCXX)" \
+		EXTRA_FLAGS="${LDFLAGS}" \
+		RELEASE_FLAGS="${CXXFLAGS}"
+}
+
+src_install() {
+	dobin bowtie2 bowtie2-*
+	exeinto /usr/share/${PN}2/scripts
+	doexe scripts/*
+
+	newman MANUAL bowtie2.1
+	dodoc AUTHORS NEWS TUTORIAL
+	dohtml doc/manual.html doc/style.css
+
+	if use examples; then
+		insinto /usr/share/${PN}2
+		doins -r example
+	fi
+}