commit: 5ca4d1505a37f273d7eaee41f89b676381e6305e Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com> AuthorDate: Sat Oct 10 19:07:16 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Wed Oct 14 12:47:58 2015 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5ca4d150
sci-biology/bowtie: Add bowtie2 in SLOT=2 sci-biology/bowtie/bowtie-2.2.6.ebuild | 54 ++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/sci-biology/bowtie/bowtie-2.2.6.ebuild b/sci-biology/bowtie/bowtie-2.2.6.ebuild new file mode 100644 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 +}
