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| -rw-r--r-- | sci-biology/bowtie/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/bowtie/bowtie-2.5.1.ebuild | 73 |
2 files changed, 74 insertions, 0 deletions
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest index e62703395825..274e5e7b9fb6 100644 --- a/sci-biology/bowtie/Manifest +++ b/sci-biology/bowtie/Manifest @@ -1 +1,2 @@ DIST bowtie2-2.4.4-source.zip 10515984 BLAKE2B be4ceb9d3155d2a9a1f580e5032251b04b89ce0c8c9c89fc3551b34fe3bd71a683362488be7aad6daef24734c6f95c19223f20e67f198f745c4432381243039c SHA512 1b5dadd7e41b90bb9b05f50bfa171fe219cfd03aa8bb6f800de4baaffeb975eef6efc4fb8b49cb0d18833f74a1741cbe1556b87388f59188e04a55dcee6a02da +DIST bowtie2-2.5.1-source.zip 10528859 BLAKE2B 9dc22bfef4b3a1cfaa606cb235acd1d7688015678d82e8ca80d3d7cf269e1f45d6cb60bc29eb334fb6f0c25d5afd8202e83a83e53668c8965857b8885d2692c8 SHA512 31cc642e318ab50e7ef6035a9c2095024d46d92a317011ed0c3ac3ccb3d427a13bf724d0158d29a4f1e07115ddcb85229b95bcb2d4351164fcadd6568293565f diff --git a/sci-biology/bowtie/bowtie-2.5.1.ebuild b/sci-biology/bowtie/bowtie-2.5.1.ebuild new file mode 100644 index 000000000000..353362fd6026 --- /dev/null +++ b/sci-biology/bowtie/bowtie-2.5.1.ebuild @@ -0,0 +1,73 @@ +# 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 +} |