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 42A21139694 for ; Mon, 15 May 2017 23:05:17 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 95845E0D39; Mon, 15 May 2017 23:05:16 +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 75265E0D39 for ; Mon, 15 May 2017 23:05:15 +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 1B1393416A3 for ; Mon, 15 May 2017 23:05:15 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id B44917452 for ; Mon, 15 May 2017 23:05:13 +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: <1494889501.c782b7fd95b50208635e1f8ff47ef3e2edc98eeb.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/SOAPdenovo2/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild X-VCS-Directories: sci-biology/SOAPdenovo2/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: c782b7fd95b50208635e1f8ff47ef3e2edc98eeb X-VCS-Branch: master Date: Mon, 15 May 2017 23:05:13 +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: 20a9f6e6-81ae-4acc-9d6d-822abb18929c X-Archives-Hash: a0db1e038c94d04529507d8d56fc5e6f commit: c782b7fd95b50208635e1f8ff47ef3e2edc98eeb Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Mon May 15 23:05:01 2017 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Mon May 15 23:05:01 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c782b7fd sci-biology/SOAPdenovo2: a bit cleanup of the build process Will need to bring in Debian med patches from git://anonscm.debian.org/debian-med/soapdenovo2.git Package-Manager: Portage-2.3.5, Repoman-2.3.2 sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild | 30 ++++++++++++++++++++++++-- 1 file changed, 28 insertions(+), 2 deletions(-) diff --git a/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild b/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild index cfd5749db..0ca68007a 100644 --- a/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild +++ b/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild @@ -3,6 +3,8 @@ EAPI=6 +inherit toolchain-funcs + DESCRIPTION="Whole genome shotgun assembler (sparse de Bruijn graph)" HOMEPAGE="https://sourceforge.net/projects/soapdenovo2 https://github.com/aquaskyline/SOAPdenovo2 @@ -14,7 +16,31 @@ SLOT="0" KEYWORDS="" IUSE="" -DEPEND="" +DEPEND="dev-libs/libaio + sci-biology/samtools:0.1-legacy" RDEPEND="${DEPEND}" -S="${WORKDIR}"/"${PN}"-src-r"${PV}" +S="${WORKDIR}"/"${PN}"-src-r"${PV}" # version is 2.04-r240 + +src_prepare(){ + # pass to broken Makefile's a proper C++ compiler through the CC variable + sed -e "s/CC = g++/CC = "$(tc-getCXX)"/;s/CFLAGS=/CFLAGS = ${CXXFLAGS} #/;s/-lbam/-lbam-0.1-legacy/" -i Makefile || die + sed -e 's#-I./sparsePregraph/inc#-I/usr/include/bam-0.1-legacy -I./sparsePregraph/inc#' -i Makefile || die + sed -e "s/CC = g++/CC = "$(tc-getCXX)"/;s/CFLAGS=/CFLAGS = ${CXXFLAGS} #/;s/-lbam/-lbam-0.1-legacy/" -i sparsePregraph/Makefile || die + sed -e 's#-I./sparsePregraph/inc#-I/usr/include/bam-0.1-legacy -I./sparsePregraph/inc#' -i sparsePregraph/Makefile || die + rm -f standardPregraph/*.a standardPregraph/inc/sam.h standardPregraph/inc/bam.h standardPregraph/inc/bgzf.h \ + sparsePregraph/inc/sam.h sparsePregraph/inc/bam.h sparsePregraph/inc/bgzf.h standardPregraph/inc/zlib.h \ + standardPregraph/inc/zconf.h sparsePregraph/inc/zlib.h sparsePregraph/inc/zconf.h standardPregraph/inc/*.so \ + sparsePregraph/*.a || die + default +} + +src_compile(){ + cd standardPregraph && emake -j1 63mer=1 + cd ../standardPregraph && emake -j1 127mer=1 + cd ../sparsePregraph && emake -j1 +} + +src_install(){ + doman "${FILESDIR}"/SOAPdenovo2.1 +}