From: "Justin Lecher" <jlec@gentoo.org>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
Date: Thu, 15 Oct 2015 17:12:30 +0000 (UTC) [thread overview]
Message-ID: <1444929139.525b717f7cebfc901579e10b1c45622bddf68eb6.jlec@gentoo> (raw)
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 <ted.tanberry@gmail.com> +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 <ted.tanberry@gmail.com> +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 <jlec@gentoo.org> metadata.xml:
- sci-biology/bowtie: Updating remote-id in metadata.xml
-
- 01 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> 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 <mmokrejs@fold.natur.cuni.cz>
- +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 <ted.tanberry@gmail.com> bowtie-1.1.1.ebuild,
- bowtie-2.2.4.ebuild: Version bump, updated ebuild, fixed small build
- system bugs
-
- 28 Sep 2013; Justin Lecher <jlec@gentoo.org> 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>
next reply other threads:[~2015-10-15 17:12 UTC|newest]
Thread overview: 7+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-10-15 17:12 Justin Lecher [this message]
-- strict thread matches above, loose matches on Subject: below --
2021-12-13 12:28 [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/ Andrew Ammerlaan
2021-03-16 18:15 Andrew Ammerlaan
2021-03-06 10:02 Andrew Ammerlaan
2019-12-23 15:38 Martin Mokrejs
2019-03-29 23:28 Martin Mokrejs
2015-02-08 21:07 Christoph Junghans
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