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 B94CB138330 for ; Tue, 9 Jan 2018 22:03:22 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id DD183E0BC0; Tue, 9 Jan 2018 22:03:21 +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 B1CBDE0BC0 for ; Tue, 9 Jan 2018 22:03:21 +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 30216335C02 for ; Tue, 9 Jan 2018 22:03:20 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 7A7F015D for ; Tue, 9 Jan 2018 22:03:18 +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: <1515535382.4dd7fc5f1806465684c1101c88021ab3e1993fa2.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/SPAdes/SPAdes-3.11.1.ebuild X-VCS-Directories: sci-biology/SPAdes/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 4dd7fc5f1806465684c1101c88021ab3e1993fa2 X-VCS-Branch: master Date: Tue, 9 Jan 2018 22:03:18 +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: 70abf0c0-5fe0-4319-af54-98d75df9a25e X-Archives-Hash: 4ffdd05b430cc3d6796dc76fde103088 commit: 4dd7fc5f1806465684c1101c88021ab3e1993fa2 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Tue Jan 9 22:03:02 2018 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Tue Jan 9 22:03:02 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4dd7fc5f sci-biology/SPAdes: version bump Try to follow the upstream's approach to compile and install the tool. src_compile() therefore does also src_install() into a DESTDIR. Package-Manager: Portage-2.3.19, Repoman-2.3.6 sci-biology/SPAdes/SPAdes-3.11.1.ebuild | 72 +++++++++++++++++++++++++++++++++ 1 file changed, 72 insertions(+) diff --git a/sci-biology/SPAdes/SPAdes-3.11.1.ebuild b/sci-biology/SPAdes/SPAdes-3.11.1.ebuild new file mode 100644 index 000000000..1842fca37 --- /dev/null +++ b/sci-biology/SPAdes/SPAdes-3.11.1.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python{2_7,3_{4,5}} ) + +inherit eutils toolchain-funcs + +DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage" +HOMEPAGE="http://cab.spbu.ru/software/spades" +SRC_URI=" + http://spades.bioinf.spbau.ru/release${PV}/SPAdes-${PV}.tar.gz + http://spades.bioinf.spbau.ru/release${PV}/manual.html -> ${P}_manual.html + http://spades.bioinf.spbau.ru/release${PV}/dipspades_manual.html -> ${P}_dipspades_manual.html + http://spades.bioinf.spbau.ru/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html + http://spades.bioinf.spbau.ru/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND=" + sys-libs/zlib + app-arch/bzip2 + dev-python/regex" +RDEPEND="${DEPEND}" +# BUG: +# SPAdes uses bundled while modified copy of dev-libs/boost (only headers are used, +# not *.so or *.a are even used) +# +# BUG: "${S}"/ext/src/ contains plenty of bundled 3rd-party tools. Drop them all and properly DEPEND on their +# existing packages +# nlopt +# llvm +# python_libs +# bamtools +# ConsensusCore +# ssw +# jemalloc +# htrie +# getopt_pp +# cppformat +# cityhash +# samtools +# bwa + +# BUG: "${S}"/ext/tools/ contains even two version of bwa, being installed as bwa-spades binary? +# bwa-0.7.12 +# bwa-0.6.2 + +pkg_pretend() { + if [[ ${MERGE_TYPE} != binary ]]; then + if [[ $(tc-getCXX) == *g++ ]] ; then + if [[ $(gcc-major-version) == 4 && $(gcc-minor-version) -lt 7 || $(gcc-major-version) -lt 4 ]] ; then + eerror "You need at least sys-devel/gcc-4.7.0" + die "You need at least sys-devel/gcc-4.7.0" + fi + fi + fi +} + +src_compile(){ + PREFIX="${ED}"/usr ./spades_compile.sh || die +} + +src_install(){ + # BUG: move *.py files to standard site-packages/ subdirectories + insinto /usr/share/"${PN}" + dodoc "${DISTDIR}"/${P}_*manual.html +}