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diff --git a/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild b/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild
new file mode 100644
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+++ b/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild
@@ -0,0 +1,75 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit flag-o-matic toolchain-funcs
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
+
+LICENSE="Artistic"
+SLOT="1"
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+IUSE="examples +tbb"
+
+RDEPEND="tbb? ( dev-cpp/tbb )"
+DEPEND="${RDEPEND}
+	sci-biology/seqan:1.4
+	app-arch/unzip"
+
+DOCS=( AUTHORS NEWS TUTORIAL doc/README )
+HTML_DOCS=( doc/{manual.html,style.css} )
+
+PATCHES=(
+	"${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
+	"${FILESDIR}/${P}-fix-setBegin-call.patch"
+	"${FILESDIR}/${P}-seqan-popcount.patch"
+	"${FILESDIR}/${P}-seqan-rename-ChunkPool.patch"
+	"${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch"
+	"${FILESDIR}/${P}-spelling.patch"
+	"${FILESDIR}/${P}-tbb-tinythread-missing.patch"
+	"${FILESDIR}/${P}-unbundle-seqan.patch"
+)
+
+src_prepare() {
+	default
+
+	# remove bundled libraries, use system seqan 1.4
+	rm -rf SeqAn-1.1/ third_party/ || die
+
+	# innocuous non-security flags, prevent log pollution
+	append-cxxflags \
+		-Wno-unused-local-typedefs \
+		-Wno-unused-but-set-variable \
+		-Wno-unused-variable
+}
+
+src_compile() {
+	emake \
+		CC="$(tc-getCC)" \
+		CPP="$(tc-getCXX)" \
+		CFLAGS="" \
+		CXXFLAGS="" \
+		EXTRA_FLAGS="${LDFLAGS}" \
+		RELEASE_FLAGS="${CXXFLAGS}" \
+		WITH_TBB="$(usex tbb 1 0)"
+}
+
+src_install() {
+	dobin ${PN} ${PN}-*
+
+	exeinto /usr/libexec/${PN}
+	doexe scripts/*
+
+	newman MANUAL ${PN}.1
+	einstalldocs
+
+	if use examples; then
+		insinto /usr/share/${PN}
+		doins -r genomes indexes
+	fi
+}