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| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-05-16 01:05:01 +0200 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-05-16 01:05:01 +0200 |
| commit | c782b7fd95b50208635e1f8ff47ef3e2edc98eeb (patch) | |
| tree | 9d88b3be7b418f4955bbc5fc5beb959aec7a3d7e | |
| parent | sci-biology/SOAPdenovo2: new package (diff) | |
| download | sci-c782b7fd95b50208635e1f8ff47ef3e2edc98eeb.tar.gz sci-c782b7fd95b50208635e1f8ff47ef3e2edc98eeb.tar.bz2 sci-c782b7fd95b50208635e1f8ff47ef3e2edc98eeb.zip | |
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
| -rw-r--r-- | sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild | 30 |
1 files 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 +} |