sci-biology/bowtie: Add bowtie2 in SLOT=2

diff --git a/sci-biology/bowtie/bowtie-2.2.6.ebuild b/sci-biology/bowtie/bowtie-2.2.6.ebuild
new file mode 100644 (file)
index 0000000..50aca7e
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-2.2.6.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data, allowing for gaps"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
+SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
+
+LICENSE="GPL-3"
+SLOT="2"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="examples cpu_flags_x86_sse2 tbb"
+REQUIRED_USE="cpu_flags_x86_sse2"
+
+RDEPEND="dev-lang/perl"
+DEPEND="${RDEPEND}
+               app-arch/unzip
+               tbb? ( dev-cpp/tbb )"
+
+S="${WORKDIR}/${PN}2-${PV}"
+
+DOCS=( AUTHORS NEWS TUTORIAL )
+HTML_DOCS=( doc/{manual.html,style.css} )
+
+src_compile() {
+       emake \
+               CC="$(tc-getCC)" \
+               CPP="$(tc-getCXX)" \
+               CFLAGS="" \
+               CXXFLAGS="" \
+               EXTRA_FLAGS="${LDFLAGS}" \
+               RELEASE_FLAGS="${CXXFLAGS} -msse2" \
+               WITH_TBB="$(usex tbb 1 0)"
+}
+
+src_install() {
+       dobin ${PN}2 ${PN}2-*
+
+       exeinto /usr/libexec/${PN}2
+       doexe scripts/*
+
+       newman MANUAL ${PN}2.1
+       einstalldocs
+
+       if use examples; then
+               insinto /usr/share/${PN}2
+               doins -r example
+       fi
+}