commit: 20633430c439732edc1dd09d5b76acefcaa54c9d Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Aug 1 16:40:40 2021 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Aug 1 16:40:40 2021 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=20633430
sci-biology/bowtie: add 2.4.4 Bug: https://bugs.gentoo.org/722870 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/bowtie/Manifest | 1 + sci-biology/bowtie/bowtie-2.4.4.ebuild | 55 ++++++++++++++++++++++++++++++++++ 2 files changed, 56 insertions(+) diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest index 50ad9715e98..96d35e2bfd2 100644 --- a/sci-biology/bowtie/Manifest +++ b/sci-biology/bowtie/Manifest @@ -1 +1,2 @@ DIST bowtie2-2.2.9-source.zip 5734235 BLAKE2B ec48e09fe05403d1085bb4e0c6ef1325b8912da0a8c942061c34f3381c6dd7ccdcc64c4bcdbb18c1da84ac57e1e34cc866fe79809c33c2769a8d75ecde7d0846 SHA512 ead8f7641f3231638d986f9e500bc4ec7afe1e542048465bfcc2e93e2b2d2e499f0dd8aa5c1e3e21df285c9d195b187682eb7e12be4a408f6c50fb97c0e0a205 +DIST bowtie2-2.4.4-source.zip 10515984 BLAKE2B be4ceb9d3155d2a9a1f580e5032251b04b89ce0c8c9c89fc3551b34fe3bd71a683362488be7aad6daef24734c6f95c19223f20e67f198f745c4432381243039c SHA512 1b5dadd7e41b90bb9b05f50bfa171fe219cfd03aa8bb6f800de4baaffeb975eef6efc4fb8b49cb0d18833f74a1741cbe1556b87388f59188e04a55dcee6a02da diff --git a/sci-biology/bowtie/bowtie-2.4.4.ebuild b/sci-biology/bowtie/bowtie-2.4.4.ebuild new file mode 100644 index 00000000000..6621b5babd9 --- /dev/null +++ b/sci-biology/bowtie/bowtie-2.4.4.ebuild @@ -0,0 +1,55 @@ +# Copyright 2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{8..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="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="cpu_flags_x86_sse2 examples" +REQUIRED_USE="cpu_flags_x86_sse2" + +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 +}
