diff options
| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-02-16 11:56:54 +0100 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-02-16 11:56:54 +0100 |
| commit | 456c869b7e5ae4d6efd1c2293b1181e59a5e6a67 (patch) | |
| tree | c2ecf23a23847d5bb0659dd12dbe1d268dd6af61 | |
| parent | sci-biology/freebayes: force compilation in a single thread as parallel build... (diff) | |
| download | sci-456c869b.tar.gz sci-456c869b.tar.bz2 sci-456c869b.zip | |
sci-biology/freebayes: respect CC/CXX/CFLAGS/CXXFLAGS
Package-Manager: Portage-2.3.3, Repoman-2.3.1
| -rw-r--r-- | sci-biology/freebayes/freebayes-9999.ebuild | 21 |
1 files changed, 19 insertions, 2 deletions
diff --git a/sci-biology/freebayes/freebayes-9999.ebuild b/sci-biology/freebayes/freebayes-9999.ebuild index 1b1eb89ed..a5e640591 100644 --- a/sci-biology/freebayes/freebayes-9999.ebuild +++ b/sci-biology/freebayes/freebayes-9999.ebuild @@ -4,7 +4,7 @@ EAPI=6 -inherit eutils git-r3 +inherit eutils git-r3 toolchain-funcs DESCRIPTION="Bayesian gen. variant detector to find short polymorphisms" HOMEPAGE="https://github.com/ekg/freebayes" @@ -15,7 +15,7 @@ SLOT="0" KEYWORDS="" IUSE="" -DEPEND="" +DEPEND="dev-util/cmake" RDEPEND="${DEPEND} sci-libs/htslib sci-biology/bamtools @@ -84,6 +84,23 @@ RDEPEND="${DEPEND} # g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../ttmath -I../bamtools/src/ -I../vcflib/src/ -I../vcflib/tabixpp/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/tabixpp/htslib -I../SeqLib -I../SeqLib/htslib -c freebayes.cpp +src_prepare(){ + find . -name Makefile | while read f; do \ + sed -e "s/-O3 -D_FILE_OFFSET_BITS=64/${CFLAGS}/" -i $f || die + sed -e "s/^CFLAGS:= -O3/CFLAGS ?= ${CFLAGS}/" -i $f || die + sed -e "s/^CXX = g++/CXX = $(tc-getCXX)/;s/^CXX=g++/CXX = $(tc-getCXX)/" -i $f || die + sed -e "s/g++ /$(tc-getCXX) /" -i $f || die + sed -e "s/-O3/${CXXFLAGS}/" -i $f || die + sed -e "s/^CC[ ]*=[ ]gcc/CC = $(tc-getCC)/" -i $f || die + sed -e "s/-g -Wall -O2/${CFLAGS}/;s/-g -Wall -Wno-unused-function -O2/${CFLAGS}/" -i $f || die + sed -e "s/-O3 /${CFLAGS}/;s/ -O3/${CFLAGS}/" -i $f || die + done + sed -e "s/^C=gcc/C = $(tc-getCC)/" -i Makefile || die + sed -e "s/gcc/$(tc-getCC)/" -i SeqLib/bwa/Makefile SeqLib/fermi-lite/Makefile || die + sed -e "s/g++/$(tc-getCXX)/" -i SeqLib/src/Makefile.am || die + default +} + src_compile(){ emake -j1 # vcflib/smithwaterman/ sometimes does not compile } |