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 5FE47139085 for ; Sun, 29 Jan 2017 18:10:15 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 4294C1455E; Sun, 29 Jan 2017 18:09:12 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id EFB091455E for ; Sun, 29 Jan 2017 18:08:56 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id C441F34164C for ; Sun, 29 Jan 2017 18:08:54 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 69AD13A0A for ; Sun, 29 Jan 2017 18:08:53 +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: <1485713320.8ef2d0632281aeb653b62b10b8da00f22f9cc62d.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/SPAdes-3.9.1.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: 8ef2d0632281aeb653b62b10b8da00f22f9cc62d X-VCS-Branch: master Date: Sun, 29 Jan 2017 18:08:53 +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: 7f1f7959-0d73-4c14-bb18-2d960a9aa36a X-Archives-Hash: 3927516cf54eb8edc8d3b586d8b76b3f commit: 8ef2d0632281aeb653b62b10b8da00f22f9cc62d Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Sun Jan 29 18:08:40 2017 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sun Jan 29 18:08:40 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8ef2d063 sci-biology/SPAdes: version bump, remove old, src_install actually does also src_compile Upstream contacted to split compile and install steps into separate procedures. The Gentoo package should be probably renamed to all lowercase letters. Hierarchy in /usr/share/spades/ is a bit awkward. Package-Manager: Portage-2.3.3, Repoman-2.3.1 .../{SPAdes-3.5.0.ebuild => SPAdes-3.9.1.ebuild} | 23 +++++++++++----------- sci-biology/SPAdes/metadata.xml | 7 ++++++- 2 files changed, 17 insertions(+), 13 deletions(-) diff --git a/sci-biology/SPAdes/SPAdes-3.5.0.ebuild b/sci-biology/SPAdes/SPAdes-3.9.1.ebuild similarity index 64% rename from sci-biology/SPAdes/SPAdes-3.5.0.ebuild rename to sci-biology/SPAdes/SPAdes-3.9.1.ebuild index 45cb010..1a5a5d5 100644 --- a/sci-biology/SPAdes/SPAdes-3.5.0.ebuild +++ b/sci-biology/SPAdes/SPAdes-3.9.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ @@ -11,8 +11,8 @@ inherit eutils toolchain-funcs DESCRIPTION="De novo de Bruijn genome assembler (bacteria to fungi) or uneven coverage" 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" + http://spades.bioinf.spbau.ru/release${PV}/SPAdes-${PV}.tar.gz + http://spades.bioinf.spbau.ru/release${PV}/manual.html -> ${P}_manual.html" LICENSE="GPL-2" SLOT="0" @@ -37,14 +37,13 @@ pkg_pretend() { fi } -src_prepare(){ - insinto /usr/share/doc/SPAdes - dodoc "${DISTDIR}"/manual.html -} +#src_compile(){ +# # grr, it actually also installs the files into $DESTDIR but that is purged before pkg_qmerge starts +# PREFIX="${D}"/usr ./spades_compile.sh || die +#} -src_compile(){ - # grr, it actually also installs the files into $PREFIX - PREFIX="${D}"/usr ./spades_compile.sh || die +src_install(){ + PREFIX="${ED}"/usr ./spades_compile.sh || die + insinto /usr/share/"${PN}" + dodoc "${DISTDIR}"/manual.html } - -# BUG: contents of "${D}" do not propagate during qmerge? diff --git a/sci-biology/SPAdes/metadata.xml b/sci-biology/SPAdes/metadata.xml index 1699e58..4baa308 100644 --- a/sci-biology/SPAdes/metadata.xml +++ b/sci-biology/SPAdes/metadata.xml @@ -5,8 +5,13 @@ mmokrejs@fold.natur.cuni.cz Martin Mokrejs - + sci-biology@gentoo.org Gentoo Biology Project + + truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads. + hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp. + dipspades is assembly module for highly polymorphic diploid genomes +