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authorMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2017-05-16 01:05:01 +0200
committerMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2017-05-16 01:05:01 +0200
commitc782b7fd95b50208635e1f8ff47ef3e2edc98eeb (patch)
tree9d88b3be7b418f4955bbc5fc5beb959aec7a3d7e
parentsci-biology/SOAPdenovo2: new package (diff)
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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.ebuild30
1 files changed, 28 insertions, 2 deletions
diff --git a/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild b/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild
index cfd5749..0ca6800 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
+}