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# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
PYTHON_COMPAT=( python2_7 python3_6 )
inherit distutils-r1
DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
HOMEPAGE="
https://github.com/pysam-developers/pysam
https://pypi.org/project/pysam/"
SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86"
RDEPEND="=sci-libs/htslib-1.5*:="
DEPEND="${RDEPEND}
dev-python/cython[${PYTHON_USEDEP}]
dev-python/setuptools[${PYTHON_USEDEP}]"
PATCHES=( "${FILESDIR}"/${PN}-0.12-fix-buildsystem.patch )
python_prepare_all() {
# unbundle htslib
export HTSLIB_MODE="external"
export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include
export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir)
rm -r htslib || die
# prevent setup.py from adding RPATHs
sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \
-i cy_build.py || die
sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
-i setup.py || die
distutils-r1_python_prepare_all
}
src_compile() {
# TODO
# empty compile, as the build system runs the whole build again in install
:
}
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