bowtie-2.5.1.ebuild
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# Copyright 2021-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 PYTHON_COMPAT=( python3_{9..11} ) inherit python-single-r1 toolchain-funcs DESCRIPTION="Popular short read aligner for Next-generation sequencing data" HOMEPAGE="https://bowtie-bio.sourceforge.net/bowtie2/" SRC_URI="mirror://sourceforge/project/${PN}-bio/bowtie2/${PV}/bowtie2-${PV}-source.zip" S="${WORKDIR}/${PN}2-${PV}" LICENSE="GPL-3" SLOT="2" KEYWORDS="~amd64 ~x86" IUSE="test cpu_flags_x86_sse2 examples" # Test script missing from tarball # ./scripts/sim/run.sh: No such file or directory RESTRICT="test" REQUIRED_USE="cpu_flags_x86_sse2 ${PYTHON_REQUIRED_USE}" RDEPEND=" ${PYTHON_DEPS} dev-lang/perl sys-libs/zlib " DEPEND="${RDEPEND}" BDEPEND=" app-arch/unzip test? ( dev-perl/App-cpanminus dev-perl/B-COW dev-perl/Clone dev-perl/Config-General dev-perl/File-Which dev-perl/local-lib dev-perl/Math-Random dev-perl/Test-Deep dev-perl/Text-Template ) " 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 } | ||