From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id C2E61138350 for ; Wed, 26 Feb 2020 08:50:22 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 0108FE08D0; Wed, 26 Feb 2020 08:50:22 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id BE4AEE08D0 for ; Wed, 26 Feb 2020 08:50:21 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 46D7134F257 for ; Wed, 26 Feb 2020 08:50:02 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id C17B710A for ; Wed, 26 Feb 2020 08:49:59 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1582706968.731ea47715109fabdd7cc3944b6c522509619f56.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild sci-biology/bowtie/bowtie-2.3.5-r1.ebuild sci-biology/bowtie/bowtie-2.3.5.1.ebuild sci-biology/bowtie/bowtie-2.4.0.ebuild X-VCS-Directories: sci-biology/bowtie/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 731ea47715109fabdd7cc3944b6c522509619f56 X-VCS-Branch: master Date: Wed, 26 Feb 2020 08:49:59 +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-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 5b7054e1-a21c-4bce-bf93-c68a4e9a58a2 X-Archives-Hash: 41c7edcc3f0c7b5368a45e7ceafd83cc commit: 731ea47715109fabdd7cc3944b6c522509619f56 Author: Martin Mokrejs gmail com> AuthorDate: Wed Feb 26 08:48:45 2020 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Feb 26 08:49:28 2020 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=731ea477 sci-biology/bowtie: version bump to 2.4.0, drop old 2.3.5 Package-Manager: Portage-2.3.87, Repoman-2.3.20 Signed-off-by: Martin Mokrejs gmail.com> .../bowtie/bowtie-1.2.2_beta20190219.ebuild | 2 +- sci-biology/bowtie/bowtie-2.3.5-r1.ebuild | 63 ---------------------- .../{bowtie-2.3.5.1.ebuild => bowtie-2.4.0.ebuild} | 2 +- 3 files changed, 2 insertions(+), 65 deletions(-) diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild index fcf0b4516..f7a1b92d4 100644 --- a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild +++ b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 diff --git a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild deleted file mode 100644 index 2a6fc04eb..000000000 --- a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild +++ /dev/null @@ -1,63 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="Popular short read aligner for Next-generation sequencing data" -HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/" -SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" -SRC_URI="https://github.com/BenLangmead/${PN}2/releases/download/v${PV}/${PN}2-${PV}-source.zip" - -LICENSE="GPL-3" -SLOT="2" -KEYWORDS="~amd64 ~x86" - -IUSE="examples cpu_flags_x86_sse2 +tbb" - -RDEPEND="dev-lang/perl - tbb? ( dev-cpp/tbb )" -DEPEND="${RDEPEND} - app-arch/unzip - sys-libs/readline" - -S="${WORKDIR}/${PN}2-${PV}" - -DOCS=( AUTHORS NEWS TUTORIAL ) -HTML_DOCS=( doc/{manual.html,style.css} ) -#PATCHES=( "${FILESDIR}/${P}-fix-c++14.patch" ) # needs 2.3.4.3 update -PATCHES=( "${FILESDIR}"/bowtie-2.3.5-fix-interleaved.patch - "${FILESDIR}"/bowtie-2.3.5-fix-fifo.patch ) - -pkg_pretend() { - if ! use cpu_flags_x86_sse2 ; then - eerror "This package requires a CPU supporting the SSE2 instruction set." - die "SSE2 support missing" - fi -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CXX="$(tc-getCXX)" \ - 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 -} diff --git a/sci-biology/bowtie/bowtie-2.3.5.1.ebuild b/sci-biology/bowtie/bowtie-2.4.0.ebuild similarity index 97% rename from sci-biology/bowtie/bowtie-2.3.5.1.ebuild rename to sci-biology/bowtie/bowtie-2.4.0.ebuild index c2fef8667..a4d6837ba 100644 --- a/sci-biology/bowtie/bowtie-2.3.5.1.ebuild +++ b/sci-biology/bowtie/bowtie-2.4.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6