From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 45D0413888F for ; Wed, 14 Oct 2015 12:48:11 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 18192E07C5; Wed, 14 Oct 2015 12:48:09 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 391DDE07C5 for ; Wed, 14 Oct 2015 12:48:08 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 5F48E3409E6 for ; Wed, 14 Oct 2015 12:48:07 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 5EE40F8E for ; Wed, 14 Oct 2015 12:48:05 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1444826878.5ca4d1505a37f273d7eaee41f89b676381e6305e.jlec@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/bowtie/bowtie-2.2.6.ebuild X-VCS-Directories: sci-biology/bowtie/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 5ca4d1505a37f273d7eaee41f89b676381e6305e X-VCS-Branch: master Date: Wed, 14 Oct 2015 12:48:05 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: fa4ee96e-2d7f-4ce9-ae61-e496e23de3ad X-Archives-Hash: df9566fbe49d0cfa8e4886a06008abed commit: 5ca4d1505a37f273d7eaee41f89b676381e6305e Author: Ted Tanberry gmail com> AuthorDate: Sat Oct 10 19:07:16 2015 +0000 Commit: Justin Lecher gentoo 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 +}