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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit eutils
DESCRIPTION="Verify and correct genome assembly scaffolds using paired-end reads"
HOMEPAGE="http://www.sanger.ac.uk/science/tools/reapr"
SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_${PV}.tar.gz
ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_1.0.18.manual.pdf"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS=""
IUSE=""
# tested smalt versions 0.6.4 to 0.7.0.1 only
DEPEND="sci-biology/bamtools
=sci-biology/samtools-0.1.19-r2" # actually bundled is 0.1.18
RDEPEND="${DEPEND}"
# sci-biology/smalt
# dev-perl/File-Basename
# dev-perl/File-Copy
# dev-perl/File-Spec
# perl-core/Getopt-Long
# dev-perl/List-Util
# dev-lang/R"
S="${WORKDIR}"/Reapr_"${PV}"
# we use temporarily patches from https://anonscm.debian.org/cgit/debian-med/reapr.git/tree/debian/patches
src_prepare(){
default
for f in "${FILESDIR}"/*.patch; do epatch $f || die; done
sed -e 's#^CC = g++#CXX ?= g++#' -i src/Makefile || die
sed -e 's#$(CC)#$(CXX)#' -i src/Makefile || die
sed -e 's#-O3##' -i src/Makefile || die
sed -e 's#^CFLAGS =#CXXFLAGS += -I../third_party/tabix -L../third_party/tabix -I../third_party/bamtools/src -L../third_party/bamtools/src#' -i src/Makefile || die
#sed -e 's#-lbamtools#../third_party/bamtools/src/libbamtools.so#' -i src/Makefile || die
sed -e 's#-ltabix#../third_party/tabix/libtabix.a#' -i src/Makefile || die
sed -e 's#CFLAGS#CXXFLAGS#' -i src/Makefile || die
}
src_compile(){
cd third_party/tabix || die
emake # to yield tabix.o object
cd ../.. || die
cd src || die
emake # link directly tabix.o but elsewhere also ../third_party/tabix/libtabix.a
}
src_install(){
dodoc "${DISTDIR}"/Reapr_"${PV}".manual.pdf
}
pkg_postinst(){
einfo "There are test data at ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_${PV}.test_data.tar.gz"
einfo "You can view results with >=sci-biology/artemis*-15.0.0"
}
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