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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="Lightweight VCF to DB framework for disease and population genetics"
HOMEPAGE="https://github.com/arq5x/gemini
http://gemini.readthedocs.org/en/latest"
SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86"
RDEPEND="
dev-python/bottle[${PYTHON_USEDEP}]
dev-python/cython[${PYTHON_USEDEP}]
dev-python/ipyparallel[${PYTHON_USEDEP}]
dev-python/jinja[${PYTHON_USEDEP}]
dev-python/networkx[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/numexpr[${PYTHON_USEDEP}]
dev-python/openpyxl[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
dev-python/pyyaml[${PYTHON_USEDEP}]
dev-python/unidecode[${PYTHON_USEDEP}]
dev-python/sqlalchemy[${PYTHON_USEDEP}]
sci-biology/bx-python[${PYTHON_USEDEP}]
sci-libs/htslib
sci-biology/pybedtools[${PYTHON_USEDEP}]
sci-biology/pysam[${PYTHON_USEDEP}]
"
distutils_enable_sphinx docs
python_prepare_all() {
# this has been renamed in newer versions of sphinx
sed -i -e 's/sphinx.ext.pngmath/sphinx.ext.imgmath/g' docs/conf.py || die
distutils-r1_python_prepare_all
}
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