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| author |   Martin Mokrejs <mmokrejs@gmail.com> | 2020-02-26 09:48:45 +0100 |
|---|---|---|
| committer | Martin Mokrejs <mmokrejs@gmail.com> | 2020-02-26 09:49:28 +0100 |
| commit | 731ea47715109fabdd7cc3944b6c522509619f56 (patch) | |
| tree | 8e6bbb333cf51e2762e9cfc0843797d1c26f393f /sci-biology | |
| parent | sci-biology/abyss: version bump (diff) | |
| download | sci-731ea47715109fabdd7cc3944b6c522509619f56.tar.gz sci-731ea47715109fabdd7cc3944b6c522509619f56.tar.bz2 sci-731ea47715109fabdd7cc3944b6c522509619f56.zip | |
sci-biology/bowtie: version bump to 2.4.0, drop old 2.3.5
Package-Manager: Portage-2.3.87, Repoman-2.3.20
Signed-off-by: Martin Mokrejs <mmokrejs@gmail.com>
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/bowtie/Manifest | 3 | ||||
| -rw-r--r-- | sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild | 2 | ||||
| -rw-r--r-- | sci-biology/bowtie/bowtie-2.3.5-r1.ebuild | 63 | ||||
| -rw-r--r-- | sci-biology/bowtie/bowtie-2.4.0.ebuild (renamed from sci-biology/bowtie/bowtie-2.3.5.1.ebuild) | 2 |
4 files changed, 3 insertions, 67 deletions
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest index b566d1c73..24665f0f9 100644 --- a/sci-biology/bowtie/Manifest +++ b/sci-biology/bowtie/Manifest @@ -1,2 +1 @@ -DIST bowtie-2.3.5.1.tar.gz 10587039 BLAKE2B e59b1ffc6360c7e81d902f481a1cdc3725b7780a49fc68642a6dd2295839d9c78378e21de175ee9c733e3822a7586a55b66d40db255dfeafbc1f2938d12f58c1 SHA512 65a3c77ca4d68e73fac464d3c60caeeab7c842c9ecd1d91ef005a15e911f7c1f51afe16a1eee5cba86bf880c157998b1200e49fb0e49b9b1b82959cfeb18fea8 -DIST bowtie2-2.3.5-source.zip 14739842 BLAKE2B eb34004c6f9ed29e4c204d92973bd089708247cb816e695f7df85d05ee336fc62ed11130a3cfbbacca8bb8cdc9af279e67d0457d28d6c3b0d2aa3e8a79b92a11 SHA512 8b16a9f3ff324f379afed204ebcd0b71a3123a6d5eab7f8832835d9ba509a5013ce66bb65189728a2c23615b6f49b9e488847fa8d054e2ae6c9658d99470549e +DIST bowtie-2.4.0.tar.gz 10588595 BLAKE2B ccbdf84bd92c792cf57819affaadcff35edd76b719bcda7cc6b68acc11592e0e14069580d1ce5e98026e03377f0920ea1e886531aeb7d6e9d5201ecbf25a6f0c SHA512 e8e72b97401db67775b44fc574d105b7acde3a27290139d846095b00270e9b4e01c0f067271d58b01e4bc8c13a3796953e8eb3b9635d5830d309f44f9ae35f35 diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild index fcf0b4516..f7a1b92d4 100644 --- a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild +++ b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 diff --git a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild deleted file mode 100644 index 2a6fc04eb..000000000 --- a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild +++ /dev/null @@ -1,63 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="Popular short read aligner for Next-generation sequencing data" -HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/" -SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" -SRC_URI="https://github.com/BenLangmead/${PN}2/releases/download/v${PV}/${PN}2-${PV}-source.zip" - -LICENSE="GPL-3" -SLOT="2" -KEYWORDS="~amd64 ~x86" - -IUSE="examples cpu_flags_x86_sse2 +tbb" - -RDEPEND="dev-lang/perl - tbb? ( dev-cpp/tbb )" -DEPEND="${RDEPEND} - app-arch/unzip - sys-libs/readline" - -S="${WORKDIR}/${PN}2-${PV}" - -DOCS=( AUTHORS NEWS TUTORIAL ) -HTML_DOCS=( doc/{manual.html,style.css} ) -#PATCHES=( "${FILESDIR}/${P}-fix-c++14.patch" ) # needs 2.3.4.3 update -PATCHES=( "${FILESDIR}"/bowtie-2.3.5-fix-interleaved.patch - "${FILESDIR}"/bowtie-2.3.5-fix-fifo.patch ) - -pkg_pretend() { - if ! use cpu_flags_x86_sse2 ; then - eerror "This package requires a CPU supporting the SSE2 instruction set." - die "SSE2 support missing" - fi -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CXX="$(tc-getCXX)" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS} -msse2" \ - WITH_TBB="$(usex tbb 1 0)" -} - -src_install() { - dobin ${PN}2 ${PN}2-* - - exeinto /usr/libexec/${PN}2 - doexe scripts/* - - newman MANUAL ${PN}2.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN}2 - doins -r example - fi -} diff --git a/sci-biology/bowtie/bowtie-2.3.5.1.ebuild b/sci-biology/bowtie/bowtie-2.4.0.ebuild index c2fef8667..a4d6837ba 100644 --- a/sci-biology/bowtie/bowtie-2.3.5.1.ebuild +++ b/sci-biology/bowtie/bowtie-2.4.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 |