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# Copyright 1999-2025 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
DOCS_BUILDER="doxygen"
DOCS_CONFIG_NAME="doxygen.conf"
PYTHON_COMPAT=( python3_{12..13} )
inherit docs python-any-r1 toolchain-funcs
DESCRIPTION="Eukaryotic gene predictor"
HOMEPAGE="https://bioinf.uni-greifswald.de/augustus/"
SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
S="${WORKDIR}/${P^}"
LICENSE="Artistic"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="test"
RESTRICT="!test? ( test )"
RDEPEND="
dev-db/sqlite:3
dev-db/mysql++:=
dev-db/mysql-connector-c:=
dev-libs/boost:=[zlib]
sci-biology/bamtools:=
sci-biology/samtools:0
sci-libs/gsl:=
sci-libs/htslib:=
sci-libs/suitesparse
sci-mathematics/lpsolve:=
sys-libs/zlib
"
DEPEND="${RDEPEND}"
BDEPEND="
test? (
${PYTHON_DEPS}
)
"
PATCHES=(
"${FILESDIR}"/augustus-3.4.0-missing-cstdint.patch
"${FILESDIR}"/augustus-3.5.0-fix-gcc15.patch
)
pkg_setup() {
use test && python-any-r1_pkg_setup
}
src_compile() {
tc-export CC CXX AR
emake
# Vendored gtest
use test && emake -C src unittest
docs_compile
}
src_test() {
if use elibc_musl; then
# Upstream already does this for non-amd64 and non-linux environments
# Probably related https://github.com/Gaius-Augustus/Augustus/issues/247
# bug #873025
emake test TEST_COMPARE= TEST_HTML=
else
emake test
fi
pushd src/unittests >/dev/null || die
if use elibc_musl; then
# Float issues
./unittests --gtest_filter='-CodonEvoTest.CodonEvoRateReadWrite' || die
else
./unittests || die
fi
popd >/dev/null || die
}
src_install() {
einstalldocs
# from upstream Makefile install:
dodir "opt/${P}"
cp -a config bin scripts "${ED}/opt/${P}" || die
local file
for file in bin/*; do
dosym "../${P}/${file}" "/opt/${file}"
done
}
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