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 091671382C5 for ; Wed, 17 Mar 2021 10:37:17 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 1E714E07B3; Wed, 17 Mar 2021 10:37:16 +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 BE98FE07B3 for ; Wed, 17 Mar 2021 10:37:15 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (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 535DD33E5E4 for ; Wed, 17 Mar 2021 10:37:14 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id A2EB45B4 for ; Wed, 17 Mar 2021 10:37:12 +0000 (UTC) From: "Andrew Ammerlaan" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Andrew Ammerlaan" Message-ID: <1615977421.77a54a4d9f64ce2bfff0ef2928500cefd5cb1b9d.andrewammerlaan@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/bowtie/bowtie-1.3.0.ebuild X-VCS-Directories: sci-biology/bowtie/ X-VCS-Committer: andrewammerlaan X-VCS-Committer-Name: Andrew Ammerlaan X-VCS-Revision: 77a54a4d9f64ce2bfff0ef2928500cefd5cb1b9d X-VCS-Branch: master Date: Wed, 17 Mar 2021 10:37:12 +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: c0d8d138-4b6b-4888-8a8d-adcd07103105 X-Archives-Hash: caeb046676296a5df159e49a4e77f59f commit: 77a54a4d9f64ce2bfff0ef2928500cefd5cb1b9d Author: Andrew Ammerlaan riseup net> AuthorDate: Wed Mar 17 10:37:01 2021 +0000 Commit: Andrew Ammerlaan riseup net> CommitDate: Wed Mar 17 10:37:01 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=77a54a4d sci-biology/bowtie: add version 1.3.0 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> sci-biology/bowtie/bowtie-1.3.0.ebuild | 63 ++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) diff --git a/sci-biology/bowtie/bowtie-1.3.0.ebuild b/sci-biology/bowtie/bowtie-1.3.0.ebuild new file mode 100644 index 000000000..118cc1303 --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.3.0.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/" +SRC_URI="https://github.com/BenLangmead/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="Artistic" +SLOT="1" +KEYWORDS="~amd64 ~x86" + +IUSE="examples +tbb" + +RDEPEND="tbb? ( dev-cpp/tbb )" +DEPEND="${RDEPEND} + app-arch/unzip" +# sci-biology/seqan:1.4" + +DOCS=( AUTHORS NEWS TUTORIAL doc/README ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +src_prepare() { + default + + # remove bundled library of headers, use system seqan 1.4 + # rm -rf SeqAn-1.1/ third_party/ || die + + # innocuous non-security flags, prevent log pollution + append-cxxflags \ + -Wno-unused-local-typedefs \ + -Wno-unused-but-set-variable \ + -Wno-unused-variable +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS}" \ + WITH_TBB="$(usex tbb 1 0)" +} + +src_install() { + dobin ${PN} ${PN}-* + + exeinto /usr/libexec/${PN} + doexe scripts/* + + newman MANUAL ${PN}.1 + einstalldocs + + if use examples; then + insinto /usr/share/${PN} + doins -r genomes indexes + fi +}