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# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit cmake-utils git-r3 multilib
DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
HOMEPAGE="http://www.cs.cmu.edu/~ckingsf/software/sailfish/"
SRC_URI=""
EGIT_REPO_URI="https://github.com/kingsfordgroup/sailfish.git"
LICENSE="GPL-3"
SLOT="0"
IUSE=""
PATCHES=( "${FILESDIR}"/${PN}-0.9.2-no-boost-static.patch )
DEPEND="dev-libs/boost:0
dev-libs/jemalloc
dev-cpp/tbb
sci-biology/jellyfish:2"
RDEPEND="${DEPEND}"
# TODO: disable running wget/curl during src_compile
# https://github.com/kingsfordgroup/sailfish/issues/80
# contains bundled RapMap https://github.com/COMBINE-lab/RapMap
# contains bundled libdivsufsort
# contains bundled libgff https://github.com/COMBINE-lab/libgff
# contains bundled jellyfish-2.2.5
# contains bundled sparsehash-2.0.2
src_install() {
cmake-utils_src_install
rm -r "${ED}"/usr/tests || die
rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die
}
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