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 B3DCC139694 for ; Sun, 14 May 2017 18:49:03 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id BD87521C03E; Sun, 14 May 2017 18:49:01 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (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 9A67821C03E for ; Sun, 14 May 2017 18:49:00 +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 AF2F73416A3 for ; Sun, 14 May 2017 18:48:59 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 524187448 for ; Sun, 14 May 2017 18:48:58 +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: <1494787726.4036ac0a6d0616ae423c7de5f5f6dfc60bd83e6f.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-3.10.1.ebuild X-VCS-Directories: sci-biology/SPAdes/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 4036ac0a6d0616ae423c7de5f5f6dfc60bd83e6f X-VCS-Branch: master Date: Sun, 14 May 2017 18:48:58 +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: 48d14f78-c26f-4557-bcfc-974532865a4d X-Archives-Hash: 323b69c0155a639b567e67bbe8b688bd commit: 4036ac0a6d0616ae423c7de5f5f6dfc60bd83e6f Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Sun May 14 18:48:46 2017 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sun May 14 18:48:46 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4036ac0a sci-biology/SPAdes: drop DEPENDency on boost Upstream says SPAdes uses bundled while modified local copy. Fix URL to new official site. Package-Manager: Portage-2.3.5, Repoman-2.3.2 sci-biology/SPAdes/SPAdes-3.10.1.ebuild | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild index de93157a4..a887fe909 100644 --- a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild +++ b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild @@ -5,10 +5,10 @@ EAPI=6 PYTHON_COMPAT=( python{2_7,3_{4,5}} ) -inherit eutils toolchain-funcs +inherit eutils toolchain-funcs cmake-utils DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage" -HOMEPAGE="http://bioinf.spbau.ru/en/spades" +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 -> ${P}_manual.html @@ -24,10 +24,11 @@ IUSE="" DEPEND=" sys-libs/zlib app-arch/bzip2 - dev-python/regex - dev-libs/boost" + dev-python/regex" RDEPEND="${DEPEND}" - +# BUG: +# SPAdes uses bundled while modified copy of dev-libs/boost +# # BUG: "${S}"/ext/src/ contains plenty of bundled 3rd-party tools. Drop them all and properly DEPEND on their # existing packages # nlopt @@ -44,7 +45,7 @@ RDEPEND="${DEPEND}" # samtools # bwa -# BUG: "${S}"/ext/tools/ contains even two version of bwa +# BUG: "${S}"/ext/tools/ contains even two version of bwa, being installed as bwa-spades binary? # bwa-0.7.12 # bwa-0.6.2 @@ -76,6 +77,7 @@ src_compile(){ src_install(){ cd build_spades || die emake install PREFIX="${ED}"/usr + # cmake-utils_src_install # dies with "${S}" does not appear to contain CMakeLists.txt # BUG: move *.py files to standard site-packages/ subdirectories insinto /usr/share/"${PN}" dodoc "${DISTDIR}"/${P}_*manual.html