commit: c782b7fd95b50208635e1f8ff47ef3e2edc98eeb Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Mon May 15 23:05:01 2017 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> 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 +}
