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# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
inherit toolchain-funcs
DESCRIPTION="Bisulfite-treated Reads Analysis Tool (short read mapper)"
HOMEPAGE="http://compbio.cs.ucr.edu/brat/"
SRC_URI="http://compbio.cs.ucr.edu/${PN}/downloads/${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
src_prepare() {
default
sed \
-e "s:g++:$(tc-getCXX):g" \
-e "s:-O3:${CFLAGS} ${LDFLAGS}:g" \
-e "s:-w:-Wall:g" \
-i Makefile || die
}
src_test() {
cd test_quick_start || die
ebegin "unpacking test files"
tar xzf test_data.tgz || die
eend $?
../brat -r references.txt -1 test_reads1.txt -2 test_reads2.txt -o output.txt -bs -pe -i 200 -a 300 || die
../brat -r references.txt -s test_reads1.txt -o output_singles1.txt -bs || die
../brat -r references.txt -s test_reads2.txt -o output_singles2.txt -bs -A || die
}
src_install() {
dobin ${PN} ${PN}-large trim acgt-count ${PN}-large-build rev-compl check-strands remove-dupl convert-to-sam
dodoc BRAT_USER_MANUAL_*.pdf
}