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# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
PYTHON_COMPAT=( python3_{7,8,9} )
inherit distutils-r1
DESCRIPTION="Correct misassemblies using linked reads from 10x Genomics Chromium"
HOMEPAGE="https://github.com/bcgsc/tigmint https://bcgsc.github.io/tigmint/"
SRC_URI="https://github.com/bcgsc/tigmint/releases/download/v${PV}/${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS=""
RESTRICT="test"
RDEPEND="
dev-python/intervaltree[${PYTHON_USEDEP}]
sci-biology/pybedtools[${PYTHON_USEDEP}]
sci-biology/pysam[${PYTHON_USEDEP}]
app-arch/pigz
sci-biology/samtools
sci-biology/minimap2
sci-biology/seqtk
"
distutils_enable_tests pytest
# install the executable into /usr/bin
# BUG: the read_fasta.py should be installed into python modules
# so it can be imported into python
src_prepare(){
sed -i Makefile -e 's#prefix=/usr/local#prefix=/usr#'
default
}
src_configure(){
python_setup
default
}
# do not run src_compile step as it runs git, makefile2graph, gsed, tred
src_install(){
default
distutils-r1_src_install
}
src_test(){
default
python_foreach_impl python_test
}
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