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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} )
inherit python-r1
DESCRIPTION="Align DNA reads to a population of genomes"
HOMEPAGE="
https://ccb.jhu.edu/software/hisat2
https://github.com/DaehwanKimLab/hisat2"
SRC_URI="https://github.com/DaehwanKimLab/hisat2/archive/v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_x86_sse2"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}"
RDEPEND="${DEPEND}"
PATCHES=( "${FILESDIR}"/${P}-respect_CXXFLAGS.patch )
# TODO: could depend on sci-biology/ncbi-tools++ or sra_sdk containing ncbi-vdb
# For the support of SRA data access in HISAT2, please download and install the [NCBI-NGS] toolkit.
# When running `make`, specify additional variables as follow.
# `make USE_SRA=1 NCBI_NGS_DIR=/path/to/NCBI-NGS-directory NCBI_VDB_DIR=/path/to/NCBI-NGS-directory`,
# where `NCBI_NGS_DIR` and `NCBI_VDB_DIR` will be used in Makefile for -I and -L compilation options.
# For example, $(NCBI_NGS_DIR)/include and $(NCBI_NGS_DIR)/lib64 will be used.
src_configure(){
if use cpu_flags_x86_sse2; then
SSE_FLAGS='-msse2'
fi
if [ "$ARCH" = "amd64" ] || [ "$ARCH" = "ia64" ] || [ "$ARCH" = "ppc64" ]; then
BITS='-m64'
else
BITS='-32'
fi
}
src_compile(){
emake SSE_FLAG="${SSE_FLAGS}" BITS="${BITS}"
}
src_install(){
dobin hisat2{,-build,-inspect,-build-s,-build-l,-align-s,-align-l,-inspect-s,-inspect-l}
python_foreach_impl python_doscript *.py
insinto /usr/share/"${PN}"/scripts
doins scripts/*.sh
dodoc MANUAL TUTORIAL
}
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