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# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
inherit perl-functions
DESCRIPTION="Genotype variant discovery without reference sequence"
HOMEPAGE="http://cortexassembler.sourceforge.net/index_cortex_var.html" # no https
SRC_URI="
https://sourceforge.net/projects/cortexassembler/files/cortex_var/latest/CORTEX_release_v${PV}.tgz
http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS=""
# http://www.well.ox.ac.uk/project-stampy
DEPEND="
sci-biology/vcftools
sci-libs/gsl
sci-libs/htslib:0=
dev-lang/perl"
RDEPEND="${DEPEND}"
S="${WORKDIR}/CORTEX_release_v${PV}"
src_prepare(){
default
sed -i -e "s/ -O3 / ${CFLAGS} /" Makefile || die
sed -i -e "s#libs/gsl-1.15#${EPREFIX}/usr/include/gsl#" Makefile || die
}
src_compile(){
rm -rf libs/htslib libs/gsl-1.15 || die
emake -C libs/string_buffer
emake STRING_BUF_PATH="${S}/libs/string_buffer" HTS_PATH="/usr/include/" -C libs/seq_file
emake NUM_COLS=1 MAXK=31 cortex_var
}
src_install(){
bash install.sh || die
perl_set_version
perl_domodule scripts/analyse_variants/bioinf-perl/lib/* scripts/calling/*
echo \
"PATH=${EPREFIX}/usr/share/${PN}/scripts/analyse_variants/needleman_wunsch" \
> "${T}/99${PN}" || die
doenvd "${T}/99${PN}"
dodoc "${DISTDIR}"/cortex_var_user_manual.pdf
}
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