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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module eutils toolchain-funcs
DESCRIPTION="Assemble and compare genotype variants (variant discovery without reference sequence)"
HOMEPAGE="http://cortexassembler.sourceforge.net/index_cortex_var.html"
SRC_URI="http://sourceforge.net/projects/cortexassembler/files/cortex_var/latest/CORTEX_release_v1.0.5.21.tgz
http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS=""
IUSE=""
# http://www.well.ox.ac.uk/project-stampy
DEPEND="sci-biology/vcftools
sci-libs/gsl
sci-libs/htslib
dev-lang/perl"
RDEPEND="${DEPEND}"
S="${WORKDIR}"/CORTEX_release_v1.0.5.21
src_prepare(){
sed -e "s/ -O3 / ${CFLAGS} /" Makefile || die
}
src_compile(){
rm -rf libs/htslib libs/gsl-1.15
make NUM_COLS=1 MAXK=31 cortex_var || die
}
src_install(){
bash install.sh || die
perl_set_version
insinto ${VENDOR_LIB}
doins scripts/analyse_variants/bioinf-perl/lib/* scripts/calling/*
echo "PATH=/usr/share/${PN}/scripts/analyse_variants/needleman_wunsch" > "${S}/99${PN}"
doenvd "${S}/99${PN}"
dodoc "${DISTDIR}"/cortex_var_user_manual.pdf
}
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