# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2

EAPI=8

inherit cmake flag-o-matic xdg

DESCRIPTION="Filter away rRNA reads from input FASTQ files"
HOMEPAGE="https://github.com/sortmerna/sortmerna"

if [[ "${PV}" != *9999 ]] ; then
	SRC_URI="https://github.com/${PN}//${PN}/archive/refs/tags/v${PV/_/-}.tar.gz -> ${P}.tar.gz"
	S="${WORKDIR}/${P/_/-}"
	KEYWORDS="~amd64 ~x86"
else
	inherit git-r3
	EGIT_REPO_URI="https://github.com/${PN}/${PN}"
	[[ "${PV}" != 9999 ]] && EGIT_BRANCH="master"
fi

LICENSE="GPL-3"
SLOT="0"
IUSE="test"

RESTRICT="!test? ( test )"
REQUIRED_USE=""

DEPEND="dev-libs/rocksdb"
RDEPEND="${DEPEND}"
BDEPEND=""

src_prepare() {
	if [[ "${PV}" != *_beta* ]] && [[ "${PV}" != *9999 ]] && [[ ! -f .version ]] ; then
		printf '%s' "${PV}" > .version || die
	fi
	cmake_src_prepare
}

src_configure() {
	local mycmakeargs=(
		-DWITH_TESTS="$(usex test)"
		-DWITH_SYSTEM_ROCKSDB:BOOL=ON
	)
	if [[ "${PV}" == *_beta* ]] ; then
		mycmakeargs+=( -DOVERRIDE_VERSION="${PV/_/-}" )
	fi
	cmake_src_configure
}

pkg_postinst(){
	einfo "You may want to fetch the databases now with"
	einfo "wget https://github.com/biocore/sortmerna/releases/download/v4.3.6/database.tar.gz"
	einfo "mkdir rRNA_databases_v4.3.6"
	einfo "tar -xvf database.tar.gz -C rRNA_databases_v4.3.6"
}