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# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
inherit cmake
DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
HOMEPAGE="https://github.com/COMBINE-lab/salmon"
SRC_URI="
https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
https://github.com/COMBINE-lab/pufferfish/archive/salmon-v${PV}.tar.gz -> pufferfish-${P}.tar.gz
https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -> libgff-${P}.tar.gz
"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64"
RDEPEND="
dev-libs/boost:=
sys-libs/zlib
"
DEPEND="${RDEPEND}
app-arch/bzip2
app-arch/xz-utils
>=dev-libs/jemalloc-5.0.1
>=dev-cpp/tbb-2018.20180312
dev-libs/cereal
sci-libs/io_lib[static-libs]
"
BDEPEND="
app-arch/unzip
net-misc/curl
"
PATCHES=(
"${FILESDIR}/${P}-find-boost.patch"
)
src_unpack() {
default
mkdir -p "${S}/external/install/lib" || die
mv "${WORKDIR}/pufferfish-${PN}-v${PV}" "${S}/external/pufferfish" || die
mv "${WORKDIR}/libgff-2.0.0" "${S}/external/libgff-2.0.0" || die
ln -s "${EPREFIX}/usr/lib64/libtbb.so" "${S}/external/install/lib/libtbb.so" || die
ln -s "${EPREFIX}/usr/lib64/libtbbmalloc.so" "${S}/external/install/lib/libtbbmalloc.so" || die
ln -s "${EPREFIX}/usr/lib64/libtbbmalloc_proxy.so" "${S}/external/install/lib/libtbbmalloc_proxy.so" || die
}
src_prepare() {
cmake_src_prepare
sed -e 's:tbb/mutex.h:oneapi/tbb/mutex.h:g' \
-i external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h \
-i external/pufferfish/external/twopaco/common/streamfastaparser.h || die
}
src_configure() {
local mycmakeargs=(
-DFETCH_BOOST=FALSE
-DBOOST_INCLUDEDIR="${EPREFIX}/usr/include/boost"
-DBOOST_LIBRARYDIR="${EPREFIX}/usr/lib64"
-DBoost_ALL_FOUND=TRUE
-Dboost_headers_FOUND=TRUE
-DBoost_FOUND=TRUE
)
cmake_src_configure
}
|
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