From 72ec06023243088ee31dacc6a9189c986c011561 Mon Sep 17 00:00:00 2001 From: Ted Tanberry Date: Sat, 10 Oct 2015 19:21:59 +0200 Subject: 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/Manifest | 1 + sci-biology/bowtie/bowtie-1.1.2.ebuild | 64 ++++++++++++++++++++++ .../bowtie-1.1.2-tbb-tinythread-missing.patch | 14 +++++ sci-biology/bowtie/metadata.xml | 5 ++ 5 files changed, 91 insertions(+) create mode 100644 sci-biology/bowtie/bowtie-1.1.2.ebuild create mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch (limited to 'sci-biology/bowtie') diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog index e05b4dc54..42bdbdfd4 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 +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 metadata.xml: sci-biology/bowtie: Updating remote-id in metadata.xml diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest index df99ece11..984902e72 100644 --- a/sci-biology/bowtie/Manifest +++ b/sci-biology/bowtie/Manifest @@ -1,3 +1,4 @@ DIST bowtie-1.1.1-src.zip 7711451 SHA256 92aacb2d32065ebee433ce76eff673c24ed12591eb6c20e22ad7e4a790c48f72 SHA512 b7e2604902d846e5e1ce79ae79eceed5401070e7db76f6875d1617e277f8244a32930b334b20869c712bab58d7d88ae26f2569350c8324df4dddae0400c013f9 WHIRLPOOL 65d1248280b32ca1f6cf7c270895abdfbec27f32128915b13a01e43a7697a743f1872440f528b29413140c260e9b7f61b6a4d435f3f83be486972b6b1533d6a5 +DIST bowtie-1.1.2-src.zip 7713258 SHA256 b1e9ccc825207efd1893d9e33244c681bcb89b9b2b811eb95a9f5a92eab637ae SHA512 3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8 WHIRLPOOL 08cb824bf7a1ddfbe6692de67191aacf44776d7d4e0ab66bd2a13ecfffd087bc28cdde4c7285c781fa4759de0a239e68f87b702bcc2e24c9b81fda5804360ce7 DIST bowtie2-2.2.3-source.zip 5724584 SHA256 c4f5ce9f0f53a6b8c7f573a26e96f6909f25bd4e0e8bd77191eaa10671baf0bf SHA512 3baf0e764a79e34b6767a62d52777fc528a82481f417ea5f1b24f38e01fac68c2870daff3060c8da11681d3270e15a10ede034356522336a94f0936d70874684 WHIRLPOOL e19ea1cee85c5ccbc198a981587e8832ebfb4bd9a02332d8171d218e89e6c84df5760db6cd1f8195b712097c6ff3ae7790415d1e63afd2632979392709de26ab DIST bowtie2-2.2.5-source.zip 5725798 SHA256 e22766dd9421c10e82a3e207ee1f0eb924c025b909ad5fffa36633cd7978d3b0 SHA512 8b97860fea73ef36a60dee3dbccdfc956ac7f619ec47a7b820d1df09cff8f77362ddc8071b59ea8021444bda59757d68bdf486fb453d5c4e4b896198bc465d60 WHIRLPOOL 7a8eb7e6d723ccb807a1db3b724326764f8f339017c0b4eb6b234e034458e736ba521106bcc8347c3c428008d8f138f463f3c3e6033b781e1c41898735c2a878 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 000000000..e4436860c --- /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 000000000..2a081ff29 --- /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 e49341707..1aef69014 100644 --- a/sci-biology/bowtie/metadata.xml +++ b/sci-biology/bowtie/metadata.xml @@ -5,4 +5,9 @@ bowtie-bio + + Enables building bowtie with the Intel + Threading Building Blocks from dev-cpp/tbb. This + flag is recommended. + -- cgit v1.2.3-65-gdbad