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# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
PYTHON_COMPAT=( python3_{10..10} )
DISTUTILS_USE_SETUPTOOLS=no
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="~amd64 ~x86"
RESTRICT="test"
PROPERTIES="test_network"
RDEPEND="
dev-python/intervaltree[${PYTHON_USEDEP}]
sci-biology/pybedtools[${PYTHON_USEDEP}]
sci-biology/pysam[${PYTHON_USEDEP}]
app-arch/pigz
app-shells/zsh
sci-biology/samtools
sci-biology/minimap2
sci-biology/seqtk
"
distutils_enable_tests pytest
src_prepare(){
# install the executable into /usr/bin
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
python_install() {
# This is a bit unorthodox, but it allows us to get both a symlink from
# /usr/bin to our script using the correct python implementation
# *and* to import it from the python shell
python_domodule bin/*.py
python_domodule bin/tigmint-arcs-tsv
python_domodule bin/tigmint-cut
python_doscript bin/*.py
python_doscript bin/tigmint-arcs-tsv
python_doscript bin/tigmint-cut
}
python_install_all() {
dobin bin/tigmint
dobin bin/tigmint-make
}
src_test(){
default
distutils-r1_src_test
}
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