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diff --git a/sci-biology/bowtie/bowtie-0.9.9.ebuild b/sci-biology/bowtie/bowtie-0.9.9.ebuild
new file mode 100644
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+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/maq/maq-0.7.1.ebuild,v 1.3 2009/02/26 17:36:19 weaver Exp $
+
+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"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de)
+# FIXME: Requires patching for gcc 4.3
+
+src_unpack() {
+	unpack ${A}
+	sed -i 's/$(CXX) $(RELEASE_FLAGS)/$(CXX) $(CXXFLAGS) $(RELEASE_FLAGS)/' "${S}/Makefile"
+}
+
+src_install() {
+	dobin bowtie bowtie-* || die
+	newman MANUAL bowtie.1
+	dodoc AUTHORS NEWS TUTORIAL
+}