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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
AUTOTOOLS_AUTORECONF=yes
inherit toolchain-funcs git-r3
DESCRIPTION="C/C++ library for working with human genetic variation data"
HOMEPAGE="http://atgu.mgh.harvard.edu/plinkseq"
EGIT_REPO_URI="https://bitbucket.org/statgen/plinkseq.git"
# https://bitbucket.org/statgen/plinkseq/commits/all
# http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml
LICENSE="GPL-2"
SLOT="0"
KEYWORDS=""
IUSE=""
DEPEND="sys-libs/zlib
dev-libs/protobuf
www-servers/mongoose
!sci-biology/fsl" # file collision on /usr/bin/mm
RDEPEND="${DEPEND}"
src_prepare(){
sed -e "s/gcc/$(tc-getCC)/g;s/g++/$(tc-getCXX)/g;s/-O3/${CFLAGS}/g" -i config_defs.Makefile || die
sed -e "s/= -static/=/g" -i config_defs.Makefile || die
rm -rf sources/ext/protobuf-* || die
rm sources/ext/protobuf sources/ext/sources/include/google || die
rm -rf sources/mongoose || die
sed -e 's@^all:.*@all: # skipping compilation of bundled dev-libs/protobuf@' -i sources/ext/Makefile || die
find . -name \*.proto | while read f; do \
d=`dirname $f`; \
pushd $d; \
protoc --cpp_out=. *.proto || exit 255; \
popd; \
done || die
#
# recopy the updated files
cp -p sources/plinkseq/sources/lib/matrix.pb.h sources/plinkseq/sources/include/plinkseq/matrix.pb.h || die
cp -p sources/plinkseq/sources/lib/variant.pb.h sources/plinkseq/sources/include/plinkseq/variant.pb.h || die
sed -e 's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g' -i sources/plinkseq/sources/lib/matrix.pb.cpp || die
sed -e 's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g' -i sources/plinkseq/sources/lib/variant.pb.cpp || die
local myinc=`pkg-config protobuf --variable=includedir`
sed -e "s@\$(PROTOBUF_LIB_BASE_DIR)/\$(INC_DIR)/@$myinc@" -i Makefile || die
local mylib=`pkg-config protobuf --variable=libdir`
sed -e "s@$(PROTOBUF_LIB_BASE_DIR)/$(BLD_LIB_DIR)/@$mylib@" -i Makefile || die
local mylibs=`pkg-config protobuf --libs`
sed -e "s@libprotobuf.a@$mylibs@" -i Makefile || die
}
src_install(){
cd build/execs || die
# TODO: avoid file collision with sci-biology/fsl
# https://bitbucket.org/statgen/plinkseq/issue/9/rename-mm-filename-to-plinkseq_mm
# TODO: avoid file collision with www-servers/mongoose
dobin gcol browser pseq behead mm smp tab2vcf pdas
}
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