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 54DC813888F for ; Mon, 12 Oct 2015 06:52:03 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id EB7C221C015; Mon, 12 Oct 2015 06:52:02 +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 9A94E21C015 for ; Mon, 12 Oct 2015 06:51:52 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id D90FC33BEBE for ; Mon, 12 Oct 2015 06:51:51 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 1D6ACE76 for ; Mon, 12 Oct 2015 06:51:44 +0000 (UTC) From: "Marius Brehler" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Marius Brehler" Message-ID: <1444499328.87642b198308aa88ce351b935b79a58a08cf164b.marbre@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/bowtie/ChangeLog sci-biology/bowtie/bowtie-2.2.6.ebuild X-VCS-Directories: sci-biology/bowtie/ X-VCS-Committer: marbre X-VCS-Committer-Name: Marius Brehler X-VCS-Revision: 87642b198308aa88ce351b935b79a58a08cf164b X-VCS-Branch: master Date: Mon, 12 Oct 2015 06:51:44 +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: 651ec90a-b496-4a65-919b-7f27ef3ea47d X-Archives-Hash: bd7018805f874ae0c0ec7f0ef4693dd6 commit: 87642b198308aa88ce351b935b79a58a08cf164b Author: Ted Tanberry gmail com> AuthorDate: Sat Oct 10 17:48:48 2015 +0000 Commit: Marius Brehler linux sungazer de> CommitDate: Sat Oct 10 17:48:48 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=87642b19 sci-biology/bowtie: Version bump to 2.2.6 dev-cpp/tbb is now supported with 'tbb' USE flag. sci-biology/bowtie/ChangeLog | 6 ++++ sci-biology/bowtie/bowtie-2.2.6.ebuild | 54 ++++++++++++++++++++++++++++++++++ 2 files changed, 60 insertions(+) diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog index 42bdbdf..6530be0 100644 --- a/sci-biology/bowtie/ChangeLog +++ b/sci-biology/bowtie/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Id$ +*bowtie-2.2.6 (10 Oct 2015) + + 10 Oct 2015; Ted Tanberry +bowtie-2.2.6.ebuild: + sci-biology/bowtie: Version bump to 2.2.6, support dev-cpp/tbb with + USE flag. + *bowtie-1.1.2 (10 Oct 2015) 10 Oct 2015; Ted Tanberry +bowtie-1.1.2.ebuild, 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..fce2985 --- /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="Short read aligner supporting gaps, matches to N nucleotides, no end-to-end requirement" +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 +}