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# Copyright 2021-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
PYTHON_COMPAT=( python3_10 )
inherit python-single-r1 toolchain-funcs
DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
SRC_URI="https://downloads.sourceforge.net/project/${PN}-bio/bowtie2/${PV}/bowtie2-${PV}-source.zip"
S="${WORKDIR}/${PN}2-${PV}"
LICENSE="GPL-3"
SLOT="2"
KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_x86_sse2 examples"
REQUIRED_USE="cpu_flags_x86_sse2 ${PYTHON_REQUIRED_USE}"
RDEPEND="
${PYTHON_DEPS}
dev-lang/perl
sys-libs/zlib"
DEPEND="${RDEPEND}"
BDEPEND="app-arch/unzip"
src_compile() {
emake \
CXX="$(tc-getCXX)" \
CXXFLAGS="" \
CPPFLAGS="${CPPFLAGS}" \
EXTRA_FLAGS="${LDFLAGS}" \
RELEASE_FLAGS="${CXXFLAGS} -msse2"
}
src_install() {
dobin bowtie2 bowtie2-*
exeinto /usr/libexec/bowtie2
doexe scripts/*
HTML_DOCS=( doc/{manual.html,style.css} )
einstalldocs
dodoc TUTORIAL
newman MANUAL bowtie2.1
python_fix_shebang "${ED}"/usr/bin/bowtie2-{build,inspect}
if use examples; then
docinto examples
dodoc -r example/.
docompress -x /usr/share/doc/${PF}/examples
fi
}
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