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 6590858973 for ; Wed, 10 Feb 2016 15:22:58 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 77B9621C002; Wed, 10 Feb 2016 15:22:56 +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 19D3C21C002 for ; Wed, 10 Feb 2016 15:22:55 +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 9EF30340A36 for ; Wed, 10 Feb 2016 15:22:54 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 84C838DF for ; Wed, 10 Feb 2016 15:22:51 +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: <1455117619.413c2c2dd02a27666281094f516976c8c7f3f357.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-3.5.0.ebuild sci-biology/SPAdes/metadata.xml X-VCS-Directories: sci-biology/SPAdes/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 413c2c2dd02a27666281094f516976c8c7f3f357 X-VCS-Branch: master Date: Wed, 10 Feb 2016 15:22:51 +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: 62b5aba1-6205-4a9b-824b-c886a9a7f5d5 X-Archives-Hash: c81e271cd1de5a6f5e1f9a56449392c2 commit: 413c2c2dd02a27666281094f516976c8c7f3f357 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Wed Feb 10 15:20:19 2016 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Feb 10 15:20:19 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=413c2c2d sci-biology/SPAdes: new package Package-Manager: portage-2.2.26 sci-biology/SPAdes/SPAdes-3.5.0.ebuild | 48 ++++++++++++++++++++++++++++++++++ sci-biology/SPAdes/metadata.xml | 9 +++++++ 2 files changed, 57 insertions(+) diff --git a/sci-biology/SPAdes/SPAdes-3.5.0.ebuild b/sci-biology/SPAdes/SPAdes-3.5.0.ebuild new file mode 100644 index 0000000..7265909 --- /dev/null +++ b/sci-biology/SPAdes/SPAdes-3.5.0.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_7,3_2,3_3,3_4} ) + +inherit eutils toolchain-funcs + +DESCRIPTION="De novo assembler for smaller genomes (bacteria to fungi)" +HOMEPAGE="http://bioinf.spbau.ru/en/spades" +SRC_URI="http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0.tar.gz + http://spades.bioinf.spbau.ru/release3.5.0/manual.html" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="sys-libs/zlib + app-arch/bzip2 + dev-python/regex + dev-libs/boost" +RDEPEND="${DEPEND}" + +pkg_pretend() { + if [[ ${MERGE_TYPE} != binary ]]; then + if [[ $(tc-getCXX) == *g++ ]] ; then + if [[ $(gcc-major-version) == 4 && $(gcc-minor-version) -lt 7 || $(gcc-major-version) -lt 4 ]] ; then + eerror "You need at least sys-devel/gcc-4.7.0" + die "You need at least sys-devel/gcc-4.7.0" + fi + fi + fi +} + +src_prepare(){ + insinto /usr/share/doc/SPAdes + dodoc "${DISTDIR}"/manual.html +} + +src_compile(){ + # grr, it actually also installs the files into $PREFIX + PREFIX="${D}"/usr ./spades_compile.sh || die +} + +# BUG: contents of "${D}" do not propagate during qmerge? diff --git a/sci-biology/SPAdes/metadata.xml b/sci-biology/SPAdes/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/SPAdes/metadata.xml @@ -0,0 +1,9 @@ + + + + sci-biology + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + +