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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} )
DISTUTILS_USE_SETUPTOOLS=rdepend
# https://github.com/Ensembl/Bio-DB-HTS/issues/30
inherit flag-o-matic autotools distutils-r1 git-r3
DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
HOMEPAGE="https://github.com/TGAC/KAT"
EGIT_REPO_URI="https://github.com/TGAC/KAT.git"
EGIT_CHECKOUT_DIR="${WORKDIR}"/KAT-Release-"${PV}"
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_x86_sse static-libs test"
CDEPEND="
>=dev-libs/boost-1.52[${PYTHON_USEDEP}]
sys-libs/zlib
dev-python/tabulate[${PYTHON_USEDEP}]
dev-python/matplotlib[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
"
DEPEND="${CDEPEND}
test? ( sys-process/time )"
RDEPEND="${CDEPEND}"
# contains bundled and *modified* version of jellyfish-2.2.0
# (libkat_jellyfish.{a,so} and "kat_" prefixes are added to all binaries)
# https://github.com/TGAC/KAT/issues/93#issuecomment-383377666
# contains embedded sci-biology/seqan headers
PATCHES=(
"${FILESDIR}"/kat-2.4.2-ignore-bundled-deps.patch
"${FILESDIR}"/kat-2.4.2-no_static_build.patch
)
S="${WORKDIR}"/KAT-Release-"${PV}"
distutils_enable_sphinx "${S}/doc/source" --no-autodoc
distutils_enable_tests pytest
src_prepare(){
default
rm -rf deps/boost || die "Failed to zap bundled boost"
eautoreconf
}
src_configure(){
python_setup
local myconf=()
myconf+=(
--disable-gnuplot
--disable-pykat-install
$(use_enable static-libs static)
) # python3 does better image rendering, no need for gnuplot
# pass down to jellyfish-2.2.0/configure
use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) )
econf ${myconf[@]}
}
src_compile(){
default
pushd scripts >/dev/null || die
distutils-r1_src_compile
popd > /dev/null || die
}
src_install(){
default
pushd scripts >/dev/null || die
distutils-r1_src_install
popd > /dev/null || die
}
src_test(){
default
python_foreach_impl python_test
}
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