commit: 72ec06023243088ee31dacc6a9189c986c011561 Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com> AuthorDate: Sat Oct 10 17:21:59 2015 +0000 Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de> CommitDate: Sat Oct 10 17:21:59 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=72ec0602
sci-biology/bowtie: Version bump to 1.1.2 dev-cpp/tbb is now supported with 'tbb' USE flag. sci-biology/bowtie/ChangeLog | 7 +++ sci-biology/bowtie/bowtie-1.1.2.ebuild | 64 ++++++++++++++++++++++ .../bowtie-1.1.2-tbb-tinythread-missing.patch | 14 +++++ sci-biology/bowtie/metadata.xml | 5 ++ 4 files changed, 90 insertions(+) diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog index e05b4dc..42bdbdf 100644 --- a/sci-biology/bowtie/ChangeLog +++ b/sci-biology/bowtie/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Id$ +*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 diff --git a/sci-biology/bowtie/bowtie-1.1.2.ebuild b/sci-biology/bowtie/bowtie-1.1.2.ebuild new file mode 100644 index 0000000..e443686 --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.1.2.ebuild @@ -0,0 +1,64 @@ +# 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}/${P}-tbb-tinythread-missing.patch" +} + +src_compile() { + if use tbb ; then + TBB="1" + else + TBB="0" + fi + + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS}" \ + WITH_TBB="${TBB}" +} + +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/files/bowtie-1.1.2-tbb-tinythread-missing.patch b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch new file mode 100644 index 0000000..2a081ff --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch @@ -0,0 +1,14 @@ +--- 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 index e493417..1aef690 100644 --- a/sci-biology/bowtie/metadata.xml +++ b/sci-biology/bowtie/metadata.xml @@ -5,4 +5,9 @@ <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>
