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74 lines
1.5 KiB
74 lines
1.5 KiB
# Copyright 2021-2024 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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PYTHON_COMPAT=( python3_{10..11} )
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inherit python-single-r1 toolchain-funcs
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DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
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HOMEPAGE="https://bowtie-bio.sourceforge.net/bowtie2/"
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SRC_URI="https://downloads.sourceforge.net/project/${PN}-bio/bowtie2/${PV}/bowtie2-${PV}-source.zip"
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S="${WORKDIR}/${PN}2-${PV}"
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LICENSE="GPL-3"
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SLOT="2"
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KEYWORDS="~amd64 ~x86"
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IUSE="test cpu_flags_x86_sse2 examples"
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# Test script missing from tarball
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# ./scripts/sim/run.sh: No such file or directory
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RESTRICT="test"
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REQUIRED_USE="cpu_flags_x86_sse2 ${PYTHON_REQUIRED_USE}"
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RDEPEND="
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${PYTHON_DEPS}
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dev-lang/perl
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sys-libs/zlib
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"
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DEPEND="${RDEPEND}"
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BDEPEND="
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app-arch/unzip
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test? (
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dev-perl/App-cpanminus
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dev-perl/B-COW
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dev-perl/Clone
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dev-perl/Config-General
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dev-perl/File-Which
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dev-perl/local-lib
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dev-perl/Math-Random
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dev-perl/Test-Deep
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dev-perl/Text-Template
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)
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"
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src_compile() {
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emake \
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CXX="$(tc-getCXX)" \
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CXXFLAGS="" \
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CPPFLAGS="${CPPFLAGS}" \
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EXTRA_FLAGS="${LDFLAGS}" \
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RELEASE_FLAGS="${CXXFLAGS} -msse2"
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}
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src_install() {
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dobin bowtie2 bowtie2-*
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exeinto /usr/libexec/bowtie2
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doexe scripts/*
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HTML_DOCS=( doc/{manual.html,style.css} )
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einstalldocs
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dodoc TUTORIAL
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newman MANUAL bowtie2.1
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python_fix_shebang "${ED}"/usr/bin/bowtie2-{build,inspect}
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if use examples; then
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docinto examples
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dodoc -r example/.
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docompress -x /usr/share/doc/${PF}/examples
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fi
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}
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