commit: 525b717f7cebfc901579e10b1c45622bddf68eb6 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Thu Oct 15 17:12:19 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Thu Oct 15 17:12:19 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=525b717f
Moved to tree Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> sci-biology/bowtie/ChangeLog | 37 -------------- sci-biology/bowtie/bowtie-1.1.1.ebuild | 53 -------------------- sci-biology/bowtie/bowtie-1.1.2.ebuild | 58 ---------------------- sci-biology/bowtie/bowtie-2.2.3.ebuild | 52 ------------------- sci-biology/bowtie/bowtie-2.2.5.ebuild | 52 ------------------- sci-biology/bowtie/bowtie-2.2.6.ebuild | 54 -------------------- .../bowtie-1.1.2-tbb-tinythread-missing.patch | 14 ------ sci-biology/bowtie/metadata.xml | 13 ----- 8 files changed, 333 deletions(-) diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog deleted file mode 100644 index 6530be0..0000000 --- a/sci-biology/bowtie/ChangeLog +++ /dev/null @@ -1,37 +0,0 @@ -# ChangeLog for sci-biology/bowtie -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*bowtie-2.2.6 (10 Oct 2015) - - 10 Oct 2015; Ted Tanberry <[email protected]> +bowtie-2.2.6.ebuild: - sci-biology/bowtie: Version bump to 2.2.6, support dev-cpp/tbb with - USE flag. - -*bowtie-1.1.2 (10 Oct 2015) - - 10 Oct 2015; Ted Tanberry <[email protected]> +bowtie-1.1.2.ebuild, - +files/bowtie-1.1.2-tbb-tinythread-missing.patch, metadata.xml: - sci-biology/bowtie: Version bump to 1.1.2, support dev-cpp/tbb with - USE flag. - - 08 Jun 2015; Justin Lecher <[email protected]> metadata.xml: - sci-biology/bowtie: Updating remote-id in metadata.xml - - 01 May 2015; Martin Mokrejs <[email protected]> bowtie-1.1.1.ebuild, - bowtie-2.2.3.ebuild, bowtie-2.2.5.ebuild: - sci-biology/bowtie: clarified package descriptions (bowtie1 vs. bowtie2) - -*bowtie-2.2.3 (27 Apr 2015) -*bowtie-2.2.5 (27 Apr 2015) - - 27 Apr 2015; Martin Mokrejs <[email protected]> - +bowtie-2.2.3.ebuild, +bowtie-2.2.5.ebuild, -bowtie-2.2.4.ebuild: - sci-biology/bowtie: version bump - - 06 Feb 2015; Ted Tanberry <[email protected]> bowtie-1.1.1.ebuild, - bowtie-2.2.4.ebuild: Version bump, updated ebuild, fixed small build - system bugs - - 28 Sep 2013; Justin Lecher <[email protected]> bowtie-2.1.0.ebuild: - Exchange common variables, fix SRC_URI diff --git a/sci-biology/bowtie/bowtie-1.1.1.ebuild b/sci-biology/bowtie/bowtie-1.1.1.ebuild deleted file mode 100644 index 387e06c..0000000 --- a/sci-biology/bowtie/bowtie-1.1.1.ebuild +++ /dev/null @@ -1,53 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="Short read (below 50nt) aligner requiring end-to-end match, no gaps" -HOMEPAGE="http://bowtie-bio.sourceforge.net/"; -SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" - -LICENSE="Artistic" -SLOT="1" -KEYWORDS="~amd64 ~x86 ~x64-macos" - -IUSE="examples" - -DEPEND="app-arch/unzip" -RDEPEND="" - -DOCS=( AUTHORS NEWS TUTORIAL doc/README ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -src_prepare() { - # Suppress useless -Wall pollution - sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile || die -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS}" -} - -src_install() { - dobin ${PN} ${PN}-* - - exeinto /usr/libexec/${PN} - doexe scripts/* - - newman MANUAL ${PN}.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN} - doins -r genomes indexes - fi -} diff --git a/sci-biology/bowtie/bowtie-1.1.2.ebuild b/sci-biology/bowtie/bowtie-1.1.2.ebuild deleted file mode 100644 index 1988f6b..0000000 --- a/sci-biology/bowtie/bowtie-1.1.2.ebuild +++ /dev/null @@ -1,58 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="Short read (below 50nt) aligner requiring end-to-end match, no gaps" -HOMEPAGE="http://bowtie-bio.sourceforge.net/"; -SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" - -LICENSE="Artistic" -SLOT="1" -KEYWORDS="~amd64 ~x86 ~x64-macos" - -IUSE="examples tbb" - -DEPEND="app-arch/unzip - tbb? ( dev-cpp/tbb )" -RDEPEND="" - -DOCS=( AUTHORS NEWS TUTORIAL doc/README ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -src_prepare() { - # Suppress useless -Wall pollution - sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile || die - - # always include tinythread.cpp - epatch "${FILESDIR}/${P}-tbb-tinythread-missing.patch" -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS}" \ - WITH_TBB="$(usex tbb 1 0)" -} - -src_install() { - dobin ${PN} ${PN}-* - - exeinto /usr/libexec/${PN} - doexe scripts/* - - newman MANUAL ${PN}.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN} - doins -r genomes indexes - fi -} diff --git a/sci-biology/bowtie/bowtie-2.2.3.ebuild b/sci-biology/bowtie/bowtie-2.2.3.ebuild deleted file mode 100644 index fb766ec..0000000 --- a/sci-biology/bowtie/bowtie-2.2.3.ebuild +++ /dev/null @@ -1,52 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="Short read aligner supporting gaps, matches to N nucleotides, no end-to-end requirement" -HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"; -SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" - -LICENSE="GPL-3" -SLOT="2" -KEYWORDS="~amd64 ~x86" - -IUSE="examples cpu_flags_x86_sse2" -REQUIRED_USE="cpu_flags_x86_sse2" - -RDEPEND="dev-lang/perl" -DEPEND="${RDEPEND} - app-arch/unzip" - -S="${WORKDIR}/${PN}2-${PV}" - -DOCS=( AUTHORS NEWS TUTORIAL ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS} -msse2" -} - -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-2.2.5.ebuild b/sci-biology/bowtie/bowtie-2.2.5.ebuild deleted file mode 100644 index fb766ec..0000000 --- a/sci-biology/bowtie/bowtie-2.2.5.ebuild +++ /dev/null @@ -1,52 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="Short read aligner supporting gaps, matches to N nucleotides, no end-to-end requirement" -HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"; -SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" - -LICENSE="GPL-3" -SLOT="2" -KEYWORDS="~amd64 ~x86" - -IUSE="examples cpu_flags_x86_sse2" -REQUIRED_USE="cpu_flags_x86_sse2" - -RDEPEND="dev-lang/perl" -DEPEND="${RDEPEND} - app-arch/unzip" - -S="${WORKDIR}/${PN}2-${PV}" - -DOCS=( AUTHORS NEWS TUTORIAL ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS} -msse2" -} - -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-2.2.6.ebuild b/sci-biology/bowtie/bowtie-2.2.6.ebuild deleted file mode 100644 index fce2985..0000000 --- a/sci-biology/bowtie/bowtie-2.2.6.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="Short read aligner supporting gaps, matches to N nucleotides, no end-to-end requirement" -HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"; -SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" - -LICENSE="GPL-3" -SLOT="2" -KEYWORDS="~amd64 ~x86" - -IUSE="examples cpu_flags_x86_sse2 tbb" -REQUIRED_USE="cpu_flags_x86_sse2" - -RDEPEND="dev-lang/perl" -DEPEND="${RDEPEND} - app-arch/unzip - tbb? ( dev-cpp/tbb )" - -S="${WORKDIR}/${PN}2-${PV}" - -DOCS=( AUTHORS NEWS TUTORIAL ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${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/files/bowtie-1.1.2-tbb-tinythread-missing.patch b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch deleted file mode 100644 index 2a081ff..0000000 --- a/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch +++ /dev/null @@ -1,14 +0,0 @@ ---- bowtie-1.1.2/Makefile -+++ bowtie-1.1.2/Makefile -@@ -106,10 +106,7 @@ - endif - - OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \ -- edit.cpp ebwt.cpp --ifneq (1,$(WITH_TBB)) -- OTHER_CPPS += tinythread.cpp --endif -+ edit.cpp ebwt.cpp tinythread.cpp - - SEARCH_CPPS = qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp \ - log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp \ diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml deleted file mode 100644 index 1aef690..0000000 --- a/sci-biology/bowtie/metadata.xml +++ /dev/null @@ -1,13 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <herd>sci-biology</herd> - <upstream> - <remote-id type="sourceforge">bowtie-bio</remote-id> - </upstream> - <use> - <flag name='tbb'>Enables building bowtie with the Intel - Threading Building Blocks from <pkg>dev-cpp/tbb</pkg>. This - flag is recommended.</flag> - </use> -</pkgmetadata>
