From ddbfba3594bda0b32f359e057555d477ffbced1e Mon Sep 17 00:00:00 2001 From: Ted Tanberry Date: Sat, 10 Oct 2015 21:04:45 +0200 Subject: sci-biology/bowtie: version bump, SLOT major version sci-biology/bowtie is now SLOTed, in order to allow for a parallel installation with bowtie2. In addition, the latest bowtie now supports dev-cpp/tbb with 'tbb' USE flag. --- sci-biology/bowtie/Manifest | 4 +- sci-biology/bowtie/bowtie-0.12.8.ebuild | 44 ---------------- sci-biology/bowtie/bowtie-1.0.0.ebuild | 42 ---------------- sci-biology/bowtie/bowtie-1.1.2.ebuild | 58 ++++++++++++++++++++++ .../bowtie/files/bowtie-0.12.8-gcc-47.patch | 45 ----------------- .../bowtie-1.1.2-tbb-tinythread-missing.patch | 14 ++++++ sci-biology/bowtie/metadata.xml | 5 ++ 7 files changed, 79 insertions(+), 133 deletions(-) delete mode 100644 sci-biology/bowtie/bowtie-0.12.8.ebuild delete mode 100644 sci-biology/bowtie/bowtie-1.0.0.ebuild create mode 100644 sci-biology/bowtie/bowtie-1.1.2.ebuild delete mode 100644 sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch create mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch (limited to 'sci-biology') diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest index 1345a9e07e4e..1291400cabae 100644 --- a/sci-biology/bowtie/Manifest +++ b/sci-biology/bowtie/Manifest @@ -1,2 +1,2 @@ -DIST bowtie-0.12.8-src.zip 15569919 SHA256 f074a0f25e156976c4951fd69651d60caab925af9829054d107ec8b19af3082d SHA512 824eddd7db24177f7e15b90fb93a0426c2b8cee4dbcac2707f4cc7e7e42bafcad3775382b79d9b4d679e0c4b5c17a1b79ad134e91a968037336b34c6262e9c48 WHIRLPOOL 7056444822e7a0de619dcab933a7870ebe7db52008f3dbb2dd72aa189325d7ca4c353133d77150ec67c414e005a834458538f57746b13fd20f06bc7289869800 -DIST bowtie-1.0.0-src.zip 7710572 SHA256 51e434a78e053301f82ae56f4e94f71f97b19f7175324777a7305c8f88c5bac5 SHA512 d867a61c9d4caa2fbe8161b93acc9ccf04294055796a82ccf8d6456019e97299d90d9f16492f873606ae394bbc735108fc97ddf4e5d576a7376f3f9744118831 WHIRLPOOL a70d6516db8ee0c8838795e3b1df0ae1986342cee5dcafd80a39b06cb07ece79d7ebfc6e88b36625d9b33f4f42f559364f42dd4d881fd729c27eac9e673951a1 +DIST bowtie-1.1.2-src.zip 7713258 SHA256 b1e9ccc825207efd1893d9e33244c681bcb89b9b2b811eb95a9f5a92eab637ae SHA512 3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8 WHIRLPOOL 08cb824bf7a1ddfbe6692de67191aacf44776d7d4e0ab66bd2a13ecfffd087bc28cdde4c7285c781fa4759de0a239e68f87b702bcc2e24c9b81fda5804360ce7 +DIST bowtie2-2.2.6-source.zip 5728779 SHA256 1000e90cdd90c3ca43c69d0d0ad951e190d36a6981a546f430a90ce86d64bfc8 SHA512 3ab5a5475cf214affd91e0d1782fd2d6dedccd979e3c809b5dfb272726d99ff1c7b59d92e387b187a7c2e43557786a1085186ccb96588de91212caf2eb94ce4f WHIRLPOOL 4fb02b3a0d76bbee0fe9abf91a71405922568bc38e593d5740df6279bad6f8b668df0debb0a81f3d3c23623558f34d842dd662a6838cf2d7f0fc8945fd00a298 diff --git a/sci-biology/bowtie/bowtie-0.12.8.ebuild b/sci-biology/bowtie/bowtie-0.12.8.ebuild deleted file mode 100644 index c26c986ed194..000000000000 --- a/sci-biology/bowtie/bowtie-0.12.8.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -inherit eutils toolchain-funcs - -DESCRIPTION="An ultrafast memory-efficient short read aligner" -HOMEPAGE="http://bowtie-bio.sourceforge.net/" -SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" - -LICENSE="Artistic" -SLOT="0" -IUSE="" -KEYWORDS="amd64 x86 ~x64-macos" - -DEPEND="app-arch/unzip" -RDEPEND="" - -# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de) -# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS - -src_prepare() { - epatch "${FILESDIR}"/${P}-gcc-47.patch -} - -src_compile() { - unset CFLAGS - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CXX="$(tc-getCXX)" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="" -} - -src_install() { - dobin bowtie bowtie-* - exeinto /usr/share/${PN}/scripts - doexe scripts/* - newman MANUAL bowtie.1 - dodoc AUTHORS NEWS TUTORIAL -} diff --git a/sci-biology/bowtie/bowtie-1.0.0.ebuild b/sci-biology/bowtie/bowtie-1.0.0.ebuild deleted file mode 100644 index b8181190243c..000000000000 --- a/sci-biology/bowtie/bowtie-1.0.0.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="An ultrafast memory-efficient short read aligner" -HOMEPAGE="http://bowtie-bio.sourceforge.net/" -SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" - -LICENSE="Artistic" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86 ~x64-macos" - -DEPEND="app-arch/unzip" -RDEPEND="" - -src_compile() { - unset CFLAGS - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CXX="$(tc-getCXX)" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS}" -} - -src_install() { - dobin bowtie bowtie-* - exeinto /usr/share/${PN}/scripts - doexe scripts/* - - insinto /usr/share/${PN} - doins -r genomes indexes - - newman MANUAL bowtie.1 - dodoc AUTHORS NEWS TUTORIAL doc/README - dohtml doc/{manual.html,style.css} -} 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 000000000000..55eec5060787 --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.1.2.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +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/files/bowtie-0.12.8-gcc-47.patch b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch deleted file mode 100644 index 3c8a1e1d9ca4..000000000000 --- a/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch +++ /dev/null @@ -1,45 +0,0 @@ - alphabet.h | 24 ++++++++++++------------ - 1 files changed, 12 insertions(+), 12 deletions(-) - -diff --git a/alphabet.h b/alphabet.h -index b464ddf..08d0281 100644 ---- a/alphabet.h -+++ b/alphabet.h -@@ -38,6 +38,18 @@ static inline TStr reverseComplement(const TStr& s, bool color) { - return s_rc; - } - -+/// Reverse a string in-place -+template -+static inline void reverseInPlace(TStr& s) { -+ typedef typename Value::Type TVal; -+ size_t len = length(s); -+ for(size_t i = 0; i < (len>>1); i++) { -+ TVal tmp = s[i]; -+ s[i] = s[len-i-1]; -+ s[len-i-1] = tmp; -+ } -+} -+ - /** - * Reverse-complement s in-place. Ns go to Ns. - */ -@@ -69,18 +81,6 @@ static inline void reverseComplementInPlace(TStr& s, bool color) { - } - } - --/// Reverse a string in-place --template --static inline void reverseInPlace(TStr& s) { -- typedef typename Value::Type TVal; -- size_t len = length(s); -- for(size_t i = 0; i < (len>>1); i++) { -- TVal tmp = s[i]; -- s[i] = s[len-i-1]; -- s[len-i-1] = tmp; -- } --} -- - /** - * Return the reverse-complement of s. - */ 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 000000000000..2a081ff297b8 --- /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 e493417070fb..58f2d3652fa7 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