From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/bowtie/Manifest | 19 + sci-biology/bowtie/bowtie-1.1.2-r1.ebuild | 74 ++++ sci-biology/bowtie/bowtie-1.1.2.ebuild | 54 +++ sci-biology/bowtie/bowtie-2.2.6.ebuild | 60 ++++ sci-biology/bowtie/bowtie-2.2.9.ebuild | 61 ++++ .../files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch | 17 + .../files/bowtie-1.1.2-fix-setBegin-call.patch | 42 +++ .../bowtie/files/bowtie-1.1.2-seqan-popcount.patch | 24 ++ .../bowtie-1.1.2-seqan-rename-ChunkPool.patch | 382 +++++++++++++++++++++ .../bowtie-1.1.2-seqan-rename-fill-to-resize.patch | 85 +++++ .../bowtie/files/bowtie-1.1.2-spelling.patch | 48 +++ .../bowtie-1.1.2-tbb-tinythread-missing.patch | 18 + .../bowtie/files/bowtie-1.1.2-unbundle-seqan.patch | 27 ++ .../bowtie/files/bowtie-2.2.9-fix-c++14.patch | 29 ++ sci-biology/bowtie/metadata.xml | 16 + 15 files changed, 956 insertions(+) create mode 100644 sci-biology/bowtie/Manifest create mode 100644 sci-biology/bowtie/bowtie-1.1.2-r1.ebuild create mode 100644 sci-biology/bowtie/bowtie-1.1.2.ebuild create mode 100644 sci-biology/bowtie/bowtie-2.2.6.ebuild create mode 100644 sci-biology/bowtie/bowtie-2.2.9.ebuild create mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch create mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch create mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch create mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch create mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch create mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch create mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch create mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch create mode 100644 sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch create mode 100644 sci-biology/bowtie/metadata.xml (limited to 'sci-biology/bowtie') diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest new file mode 100644 index 000000000000..155be157845f --- /dev/null +++ b/sci-biology/bowtie/Manifest @@ -0,0 +1,19 @@ +AUX bowtie-1.1.2-_ContextLss-1.1-1.4.patch 601 SHA256 3fc2e55806824558c12e7d3ae3f4be77f9897f222e1de06c3ab39dff74fa7ad7 SHA512 e39ec6323cc6fee49a6ecf3565066d9cb8f8001af2701de292025f268d57dcfa3d4c35f3e2aed56b7e3835a955e5bfb595214ac232309fcc46c6d51f83cd9f2e WHIRLPOOL 5a65ab3bcf49679ff9dbc0225415a3664e924622f706605f00ea32c157b9f87f2d0eb13322f60c0b327c7395a9865515d8241ddcaf6b764a76053f67765ade24 +AUX bowtie-1.1.2-fix-setBegin-call.patch 1269 SHA256 ccf253e4b2fddef2a199e9fe2b93519f579c5b16e5a002723868ffaad3b07cc5 SHA512 8838a0d8b35c9ceb4be1ef3439eab5e3478dcfe11c5e59e327717676eceab413b07ec97dbda9fb3527ab61653a8a6e2d651b5bb4c24114288d3b07922348c5d3 WHIRLPOOL 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000000000000..d8b607f870fc --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/" +SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" + +LICENSE="Artistic" +SLOT="1" +KEYWORDS="~amd64 ~x86 ~x64-macos" + +IUSE="examples +tbb" + +RDEPEND="tbb? ( dev-cpp/tbb )" +DEPEND="${RDEPEND} + sci-biology/seqan:1.4 + app-arch/unzip" + +DOCS=( AUTHORS NEWS TUTORIAL doc/README ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +PATCHES=( + "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" + "${FILESDIR}/${P}-fix-setBegin-call.patch" + "${FILESDIR}/${P}-seqan-popcount.patch" + "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch" + "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch" + "${FILESDIR}/${P}-spelling.patch" + "${FILESDIR}/${P}-tbb-tinythread-missing.patch" + "${FILESDIR}/${P}-unbundle-seqan.patch" +) + +src_prepare() { + default + + # remove bundled libraries, use system seqan 1.4 + rm -rf SeqAn-1.1/ third_party/ || die + + # innocuous non-security flags, prevent log pollution + append-cxxflags \ + -Wno-unused-local-typedefs \ + -Wno-unused-but-set-variable \ + -Wno-unused-variable +} + +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-1.1.2.ebuild b/sci-biology/bowtie/bowtie-1.1.2.ebuild new file mode 100644 index 000000000000..1ada8a0fdc2b --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.1.2.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +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/${P}-src.zip" + +LICENSE="Artistic" +SLOT="1" +KEYWORDS="amd64 x86 ~x64-macos" + +IUSE="examples +tbb" + +DEPEND="app-arch/unzip + tbb? ( dev-cpp/tbb )" +RDEPEND="" + +DOCS=( AUTHORS NEWS TUTORIAL doc/README ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +src_prepare() { + # always include tinythread.cpp + epatch "${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-2.2.6.ebuild b/sci-biology/bowtie/bowtie-2.2.6.ebuild new file mode 100644 index 000000000000..29826473a3b3 --- /dev/null +++ b/sci-biology/bowtie/bowtie-2.2.6.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/" +SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" + +LICENSE="GPL-3" +SLOT="2" +KEYWORDS="amd64 x86" + +IUSE="examples cpu_flags_x86_sse2 +tbb" + +RDEPEND="dev-lang/perl" +DEPEND="${RDEPEND} + app-arch/unzip + tbb? ( dev-cpp/tbb )" + +S="${WORKDIR}/${PN}2-${PV}" + +DOCS=( AUTHORS NEWS TUTORIAL ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +pkg_pretend() { + if ! use cpu_flags_x86_sse2 ; then + eerror "This package requires a CPU supporting the SSE2 instruction set." + die "SSE2 support missing" + fi +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CXX="$(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/bowtie-2.2.9.ebuild b/sci-biology/bowtie/bowtie-2.2.9.ebuild new file mode 100644 index 000000000000..0bacb8ca25d7 --- /dev/null +++ b/sci-biology/bowtie/bowtie-2.2.9.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/" +SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" + +LICENSE="GPL-3" +SLOT="2" +KEYWORDS="~amd64 ~x86" + +IUSE="examples cpu_flags_x86_sse2 +tbb" + +RDEPEND="dev-lang/perl + tbb? ( dev-cpp/tbb )" +DEPEND="${RDEPEND} + app-arch/unzip" + +S="${WORKDIR}/${PN}2-${PV}" + +DOCS=( AUTHORS NEWS TUTORIAL ) +HTML_DOCS=( doc/{manual.html,style.css} ) +PATCHES=( "${FILESDIR}/${PN}-2.2.9-fix-c++14.patch" ) + +pkg_pretend() { + if ! use cpu_flags_x86_sse2 ; then + eerror "This package requires a CPU supporting the SSE2 instruction set." + die "SSE2 support missing" + fi +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CXX="$(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-_ContextLss-1.1-1.4.patch b/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch new file mode 100644 index 000000000000..78b9c01a0462 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch @@ -0,0 +1,17 @@ +Description: Change class name of _Context_LSS + New version 1.4 of SeQan uses a different name of the class. +Forwarded: no +Author: Gert Wollny +Last-Update: 2014-100-06 + +--- a/diff_sample.h ++++ b/diff_sample.h +@@ -856,7 +856,7 @@ void DifferenceCoverSample::build( + { + Timer timer(cout, " Invoking Larsson-Sadakane on ranks time: ", this->verbose()); + VMSG_NL(" Invoking Larsson-Sadakane on ranks"); +- _Context_LSS c; ++ ContextLss_ c; + c.suffixsort( + (TIndexOff*)begin(_isaPrime, Standard()), + (TIndexOff*)begin(sPrime, Standard()), diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch b/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch new file mode 100644 index 000000000000..af7f7f61cd5e --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch @@ -0,0 +1,42 @@ +Description: Proper type-casting in using seqan::_setBegin(). + Required by newer versions of GCC. +Forwarded: no +Author: Ognyan Kulev +Last-Update: 2013-04-18 + +--- a/pat.h ++++ b/pat.h +@@ -82,20 +82,20 @@ struct ReadBuf { + ~ReadBuf() { + clearAll(); reset(); + // Prevent seqan from trying to free buffers +- _setBegin(patFw, NULL); +- _setBegin(patRc, NULL); +- _setBegin(qual, NULL); +- _setBegin(patFwRev, NULL); +- _setBegin(patRcRev, NULL); +- _setBegin(qualRev, NULL); +- _setBegin(name, NULL); ++ _setBegin(patFw, (Dna5*)NULL); ++ _setBegin(patRc, (Dna5*)NULL); ++ _setBegin(qual, (char*)NULL); ++ _setBegin(patFwRev, (Dna5*)NULL); ++ _setBegin(patRcRev, (Dna5*)NULL); ++ _setBegin(qualRev, (char*)NULL); ++ _setBegin(name, (char*)NULL); + for(int j = 0; j < 3; j++) { +- _setBegin(altPatFw[j], NULL); +- _setBegin(altPatFwRev[j], NULL); +- _setBegin(altPatRc[j], NULL); +- _setBegin(altPatRcRev[j], NULL); +- _setBegin(altQual[j], NULL); +- _setBegin(altQualRev[j], NULL); ++ _setBegin(altPatFw[j], (Dna5*)NULL); ++ _setBegin(altPatFwRev[j], (Dna5*)NULL); ++ _setBegin(altPatRc[j], (Dna5*)NULL); ++ _setBegin(altPatRcRev[j], (Dna5*)NULL); ++ _setBegin(altQual[j], (char*)NULL); ++ _setBegin(altQualRev[j], (char*)NULL); + } + } + diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch new file mode 100644 index 000000000000..52cb4f496521 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch @@ -0,0 +1,24 @@ +Description: Use SeqAn 1.4's seqan::popCount() function instead of own function +Author: Ognyan Kulev +Last-Update: 2014-03-08 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- a/diff_sample.h ++++ b/diff_sample.h +@@ -476,6 +476,8 @@ static String getDeltaMap(T v, const + return amap; + } + ++// Debian: Use seqan::popCount ++#if 0 + /** + * Return population count (count of all bits set to 1) of i. + */ +@@ -488,6 +490,7 @@ static unsigned int popCount(T i) { + } + return cnt; + } ++#endif + + /** + * Calculate log-base-2 of i diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch new file mode 100644 index 000000000000..171f9bab8fae --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch @@ -0,0 +1,382 @@ +Description: Renamed ChunkPool class to bowtieChunkPool. + SeqAn has a class with the same name and fatal name collision happens. +Forwarded: no +Author: Ognyan Kulev +Last-Update: 2013-04-18 + +--- a/aligner.h ++++ b/aligner.h +@@ -337,7 +337,7 @@ public: + bool verbose, + bool quiet, + int maxBts, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + int *btCnt = NULL, + AlignerMetrics *metrics = NULL) : + Aligner(true, rangeMode), +@@ -544,7 +544,7 @@ protected: + bool quiet_; // don't print informational/warning info + + const int maxBts_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + int *btCnt_; + AlignerMetrics *metrics_; + }; +@@ -585,7 +585,7 @@ public: + bool verbose, + bool quiet, + int maxBts, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + int *btCnt) : + Aligner(true, rangeMode), + refs_(refs), +@@ -1358,7 +1358,7 @@ protected: + bool quiet_; + + int maxBts_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + int *btCnt_; + + // Range-finding state for first mate +@@ -1482,7 +1482,7 @@ public: + bool verbose, + bool quiet, + int maxBts, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + int *btCnt) : + Aligner(true, rangeMode), + refs_(refs), +@@ -2035,7 +2035,7 @@ protected: + TDriver* driver_; + + // Pool for distributing chunks of best-first path descriptor memory +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + + bool verbose_; + bool quiet_; +--- a/aligner_0mm.h ++++ b/aligner_0mm.h +@@ -32,7 +32,7 @@ public: + RangeCache* cacheFw, + RangeCache* cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector >& os, + bool maqPenalty, +@@ -124,7 +124,7 @@ private: + RangeCache *cacheFw_; + RangeCache *cacheBw_; + const uint32_t cacheLimit_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + BitPairReference* refs_; + vector >& os_; + bool maqPenalty_; +@@ -164,7 +164,7 @@ public: + RangeCache* cacheFw, + RangeCache* cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector >& os, + bool reportSe, +@@ -366,7 +366,7 @@ private: + RangeCache *cacheFw_; + RangeCache *cacheBw_; + const uint32_t cacheLimit_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + BitPairReference* refs_; + vector >& os_; + const bool reportSe_; +--- a/aligner_1mm.h ++++ b/aligner_1mm.h +@@ -32,7 +32,7 @@ public: + RangeCache *cacheFw, + RangeCache *cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector >& os, + bool maqPenalty, +@@ -161,7 +161,7 @@ private: + RangeCache *cacheFw_; + RangeCache *cacheBw_; + const uint32_t cacheLimit_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + BitPairReference* refs_; + vector >& os_; + const bool maqPenalty_; +@@ -201,7 +201,7 @@ public: + RangeCache *cacheFw, + RangeCache *cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector >& os, + bool reportSe, +@@ -478,7 +478,7 @@ private: + RangeCache *cacheFw_; + RangeCache *cacheBw_; + const uint32_t cacheLimit_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + BitPairReference* refs_; + vector >& os_; + const bool reportSe_; +--- a/aligner_23mm.h ++++ b/aligner_23mm.h +@@ -33,7 +33,7 @@ public: + RangeCache *cacheFw, + RangeCache *cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector >& os, + bool maqPenalty, +@@ -231,7 +231,7 @@ private: + RangeCache *cacheFw_; + RangeCache *cacheBw_; + const uint32_t cacheLimit_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + BitPairReference* refs_; + vector >& os_; + const bool maqPenalty_; +@@ -273,7 +273,7 @@ public: + RangeCache *cacheFw, + RangeCache *cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector >& os, + bool reportSe, +@@ -675,7 +675,7 @@ private: + RangeCache *cacheFw_; + RangeCache *cacheBw_; + const uint32_t cacheLimit_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + BitPairReference* refs_; + vector >& os_; + const bool reportSe_; +--- a/aligner_seed_mm.h ++++ b/aligner_seed_mm.h +@@ -37,7 +37,7 @@ public: + RangeCache* cacheFw, + RangeCache* cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector >& os, + bool maqPenalty, +@@ -554,7 +554,7 @@ private: + RangeCache *cacheFw_; + RangeCache *cacheBw_; + const uint32_t cacheLimit_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + BitPairReference* refs_; + vector >& os_; + bool strandFix_; +@@ -598,7 +598,7 @@ public: + RangeCache* cacheFw, + RangeCache* cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector >& os, + bool reportSe, +@@ -1375,7 +1375,7 @@ private: + RangeCache *cacheFw_; + RangeCache *cacheBw_; + const uint32_t cacheLimit_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + BitPairReference* refs_; + vector >& os_; + const bool reportSe_; +--- a/ebwt_search.cpp ++++ b/ebwt_search.cpp +@@ -111,7 +111,7 @@ static bool strandFix; // attempt to fi + static bool randomizeQuals; // randomize quality values + static bool stats; // print performance stats + static int chunkPoolMegabytes; // max MB to dedicate to best-first search frames per thread +-static int chunkSz; // size of single chunk disbursed by ChunkPool ++static int chunkSz; // size of single chunk disbursed by bowtieChunkPool + static bool chunkVerbose; // have chunk allocator output status messages? + static bool recal; + static int recalMaxCycle; +@@ -223,7 +223,7 @@ static void resetOptions() { + randomizeQuals = false; // randomize quality values + stats = false; // print performance stats + chunkPoolMegabytes = 64; // max MB to dedicate to best-first search frames per thread +- chunkSz = 256; // size of single chunk disbursed by ChunkPool (in KB) ++ chunkSz = 256; // size of single chunk disbursed by bowtieChunkPool (in KB) + chunkVerbose = false; // have chunk allocator output status messages? + recal = false; + recalMaxCycle = 64; +@@ -1201,7 +1201,7 @@ static void exactSearchWorkerStateful(vo + PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); + HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); + +- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); ++ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); + UnpairedExactAlignerV1Factory alSEfact( + ebwt, + NULL, +@@ -1385,7 +1385,7 @@ static void mismatchSearchWorkerFullStat + // Global initialization + PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); + HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); +- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); ++ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); + + Unpaired1mmAlignerV1Factory alSEfact( + ebwtFw, +@@ -1687,7 +1687,7 @@ static void twoOrThreeMismatchSearchWork + PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); + HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); + +- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); ++ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); + Unpaired23mmAlignerV1Factory alSEfact( + ebwtFw, + &ebwtBw, +@@ -2156,7 +2156,7 @@ static void seededQualSearchWorkerFullSt + // Global initialization + PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); + HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); +- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); ++ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); + + AlignerMetrics *metrics = NULL; + if(stats) { +--- a/ebwt_search_backtrack.h ++++ b/ebwt_search_backtrack.h +@@ -2724,7 +2724,7 @@ public: + bool verbose, + bool quiet, + bool mate1, +- ChunkPool* pool, ++ bowtieChunkPool* pool, + int *btCnt) : + SingleRangeSourceDriver( + params, rs, fw, sink, sinkPt, os, verbose, +@@ -2927,7 +2927,7 @@ public: + bool verbose, + bool quiet, + bool mate1, +- ChunkPool* pool, ++ bowtieChunkPool* pool, + int *btCnt = NULL) : + params_(params), + rs_(rs), +@@ -2986,7 +2986,7 @@ protected: + bool verbose_; + bool quiet_; + bool mate1_; +- ChunkPool* pool_; ++ bowtieChunkPool* pool_; + int *btCnt_; + }; + +--- a/pool.h ++++ b/pool.h +@@ -19,13 +19,13 @@ + * is set at construction time. Heap memory is only allocated at + * construction and deallocated at destruction. + */ +-class ChunkPool { ++class bowtieChunkPool { + public: + /** + * Initialize a new pool with an initial size of about 'bytes' + * bytes. Exit with an error message if we can't allocate it. + */ +- ChunkPool(uint32_t chunkSz, uint32_t totSz, bool verbose_) : ++ bowtieChunkPool(uint32_t chunkSz, uint32_t totSz, bool verbose_) : + verbose(verbose_), patid(0), pool_(NULL), cur_(0), + chunkSz_(chunkSz), totSz_(totSz), lim_(totSz/chunkSz), + bits_(lim_), exhaustCrash_(false), +@@ -38,7 +38,7 @@ public: + } + } catch(std::bad_alloc& e) { + ThreadSafe _ts(&gLock); +- std::cerr << "Error: Could not allocate ChunkPool of " ++ std::cerr << "Error: Could not allocate bowtieChunkPool of " + << totSz << " bytes" << std::endl; + exhausted(); + throw 1; // Exit if we haven't already +@@ -48,7 +48,7 @@ public: + /** + * Delete all the pools. + */ +- ~ChunkPool() { ++ ~bowtieChunkPool() { + if(pool_ != NULL) delete[] pool_; + } + +@@ -189,7 +189,7 @@ public: + * Initialize a new pool with an initial size of about 'bytes' + * bytes. Exit with an error message if we can't allocate it. + */ +- AllocOnlyPool(ChunkPool* pool, const char *name) : ++ AllocOnlyPool(bowtieChunkPool* pool, const char *name) : + pool_(pool), name_(name), curPool_(0), cur_(0) + { + assert(pool != NULL); +@@ -388,7 +388,7 @@ protected: + lastCurInPool_.pop_back(); + } + +- ChunkPool* pool_; ++ bowtieChunkPool* pool_; + const char *name_; + std::vector pools_; /// the memory pools + uint32_t curPool_; /// pool we're current allocating from +--- a/range_source.h ++++ b/range_source.h +@@ -1388,7 +1388,7 @@ class PathManager { + + public: + +- PathManager(ChunkPool* cpool_, int *btCnt, bool verbose, bool quiet) : ++ PathManager(bowtieChunkPool* cpool_, int *btCnt, bool verbose, bool quiet) : + branchQ_(verbose, quiet), + cpool(cpool_), + bpool(cpool, "branch"), +@@ -1637,7 +1637,7 @@ protected: + + public: + +- ChunkPool *cpool; // pool for generic chunks of memory ++ bowtieChunkPool *cpool; // pool for generic chunks of memory + AllocOnlyPool bpool; // pool for allocating Branches + AllocOnlyPool rpool; // pool for allocating RangeStates + AllocOnlyPool epool; // pool for allocating Edits +@@ -1811,7 +1811,7 @@ public: + bool quiet, + bool mate1, + uint32_t minCostAdjustment, +- ChunkPool* pool, ++ bowtieChunkPool* pool, + int *btCnt) : + RangeSourceDriver(true, minCostAdjustment), + len_(0), mate1_(mate1), diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch new file mode 100644 index 000000000000..38664aeee989 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch @@ -0,0 +1,85 @@ +Description: Renamed seqan::fill function calls to use seqan::resize. + SeqAn 1.3 renamed seqan::fill() to seqan::resize(). + SeqAn ticket: http://trac.seqan.de/ticket/77 +Forwarded: no +Author: Ognyan Kulev +Last-Update: 2014-08-13 + +--- a/blockwise_sa.h ++++ b/blockwise_sa.h +@@ -456,8 +456,8 @@ void KarkkainenBlockwiseSA::buildS + try { + // Allocate and initialize containers for holding bucket + // sizes and representatives. +- fill(bucketSzs, numBuckets, 0, Exact()); +- fill(bucketReps, numBuckets, OFF_MASK, Exact()); ++ resize(bucketSzs, numBuckets, 0, Exact()); ++ resize(bucketReps, numBuckets, OFF_MASK, Exact()); + } catch(bad_alloc &e) { + if(this->_passMemExc) { + throw e; // rethrow immediately +@@ -816,7 +816,7 @@ void KarkkainenBlockwiseSA::nextBl + // Not the last bucket + assert_lt(_cur, length(_sampleSuffs)); + hi = _sampleSuffs[_cur]; +- fill(zHi, _dcV, 0, Exact()); ++ resize(zHi, _dcV, 0, Exact()); + assert_eq(zHi[0], 0); + calcZ(t, hi, zHi, this->verbose(), this->sanityCheck()); + } +@@ -825,7 +825,7 @@ void KarkkainenBlockwiseSA::nextBl + assert_gt(_cur, 0); + assert_leq(_cur, length(_sampleSuffs)); + lo = _sampleSuffs[_cur-1]; +- fill(zLo, _dcV, 0, Exact()); ++ resize(zLo, _dcV, 0, Exact()); + assert_gt(_dcV, 3); + assert_eq(zLo[0], 0); + calcZ(t, lo, zLo, this->verbose(), this->sanityCheck()); +--- a/diff_sample.h ++++ b/diff_sample.h +@@ -452,7 +452,7 @@ static String getDeltaMap(T v, const + // Declare anchor-map-related items + String amap; + size_t amapEnts = 1; +- fill(amap, v, 0xffffffff, Exact()); ++ resize(amap, v, 0xffffffff, Exact()); + amap[0] = 0; + // Print out difference cover (and optionally calculate + // anchor map) +@@ -532,7 +532,7 @@ public: + assert_gt(_d, 0); + assert_eq(1, popCount(_v)); // must be power of 2 + // Build map from d's to idx's +- fill(_dInv, _v, 0xffffffff, Exact()); ++ resize(_dInv, _v, 0xffffffff, Exact()); + uint32_t lim = (uint32_t)length(_ds); + for(uint32_t i = 0; i < lim; i++) { + _dInv[_ds[i]] = i; +@@ -656,7 +656,7 @@ void DifferenceCoverSample::doBuil + VMSG_NL(" Doing sanity check"); + TIndexOffU added = 0; + String sorted; +- fill(sorted, length(_isaPrime), OFF_MASK, Exact()); ++ resize(sorted, length(_isaPrime), OFF_MASK, Exact()); + for(size_t di = 0; di < this->d(); di++) { + uint32_t d = _ds[di]; + size_t i = 0; +@@ -717,7 +717,7 @@ void DifferenceCoverSample::buildS + assert_eq(length(_doffs), d+1); + // Size sPrime appropriately + reserve(sPrime, sPrimeSz+1, Exact()); // reserve extra slot for LS +- fill(sPrime, sPrimeSz, OFF_MASK, Exact()); ++ resize(sPrime, sPrimeSz, OFF_MASK, Exact()); + // Slot suffixes from text into sPrime according to the mu + // mapping; where the mapping would leave a blank, insert a 0 + TIndexOffU added = 0; +@@ -823,7 +823,7 @@ void DifferenceCoverSample::build( + // arrays back into sPrime. + VMSG_NL(" Allocating rank array"); + reserve(_isaPrime, length(sPrime)+1, Exact()); +- fill(_isaPrime, length(sPrime), OFF_MASK, Exact()); ++ resize(_isaPrime, length(sPrime), OFF_MASK, Exact()); + assert_gt(length(_isaPrime), 0); + { + Timer timer(cout, " Ranking v-sort output time: ", this->verbose()); diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch b/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch new file mode 100644 index 000000000000..ff484dfa3ebb --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch @@ -0,0 +1,48 @@ +Author: Andreas Tille +Last-Update: Thu, 01 Oct 2015 09:47:23 +0200 +Description: Fix spelling + +--- a/MANUAL ++++ b/MANUAL +@@ -544,7 +544,7 @@ The `bowtie`, `bowtie-build` and `bowtie + actually wrapper scripts that call binary programs as appropriate. The + wrappers shield users from having to distinguish between "small" and + "large" index formats, discussed briefly in the following section. The +-appropiate index type is selected based on the input size. ++appropriate index type is selected based on the input size. + + It is recommended that you always run the bowtie wrappers and not run + the binaries directly. +--- a/MANUAL.markdown ++++ b/MANUAL.markdown +@@ -559,7 +559,7 @@ The `bowtie`, `bowtie-build` and `bowtie + actually wrapper scripts that call binary programs as appropriate. The + wrappers shield users from having to distinguish between "small" and + "large" index formats, discussed briefly in the following section. The +-appropiate index type is selected based on the input size. ++appropriate index type is selected based on the input size. + + It is recommended that you always run the bowtie wrappers and not run + the binaries directly. +--- a/doc/manual.html ++++ b/doc/manual.html +@@ -201,7 +201,7 @@ T2302111203131231130300111123220 +

Like other platforms, SOLiD supports generation of paired-end reads. When colorspace alignment is enabled, the default paired-end orientation setting is --ff. This is because most SOLiD datasets have that orientation.

+

Note that SOLiD-generated read files can have "orphaned" mates; i.e. mates without a correpsondingly-named mate in the other file. To avoid problems due to orphaned mates, SOLiD paired-end output should first be converted to .csfastq files with unpaired mates omitted. This can be accomplished using, for example, [Galaxy]'s conversion tool (click "NGS: QC and manipulation", then "SOLiD-to-FASTQ" in the left-hand sidebar).

+

Wrapper scripts

+-

The bowtie, bowtie-build and bowtie-inspect executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between "small" and "large" index formats, discussed briefly in the following section. The appropiate index type is selected based on the input size.

++

The bowtie, bowtie-build and bowtie-inspect executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between "small" and "large" index formats, discussed briefly in the following section. The appropriate index type is selected based on the input size.

+

It is recommended that you always run the bowtie wrappers and not run the binaries directly.

+

Small and large indexes

+

bowtie-build can index reference genomes of any size. For genomes less than about 4 billion nucleotides in length, bowtie-build builds a "small" index using 32-bit numbers in various parts of the index. When the genome is longer, bowtie-build builds a "large" index using 64-bit numbers. Small indexes are stored in files with the .ebwt extension, and large indexes are stored in files with the .ebwtl extension. The user need not worry about whether a particular index is small or large; the wrapper scripts will automatically build and use the appropriate index.

+--- a/ref_read.cpp ++++ b/ref_read.cpp +@@ -263,7 +263,7 @@ fastaRefReadSizes(vector& in, + << "reference into smaller chunks and index each independently." << endl; + #else + cerr << "Error: Reference sequence has more than 2^32-1 characters! Please try to" << endl +- << "build a large index instead using the appropiate options." << endl; ++ << "build a large index instead using the appropriate options." << endl; + #endif + throw 1; + } 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..bc0f1d09557d --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch @@ -0,0 +1,18 @@ +Fixes missing tinythread.cpp when using TBB: + +ebwt_search.cpp:(.text+0x91bb): undefined reference to `tthread::thread::join()' + +--- 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/files/bowtie-1.1.2-unbundle-seqan.patch b/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch new file mode 100644 index 000000000000..54391ae415a3 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch @@ -0,0 +1,27 @@ +Description: Use Debian packaged SeqAn library instead of copy in upstream source +Author: Andreas Tille +Date: 2011-01-30 +Last-Update: 2013-04-18 +Reviewed-by: Ognyan Kulev + +--- a/Makefile ++++ b/Makefile +@@ -5,9 +5,7 @@ + prefix = /usr/local + bindir = $(prefix)/bin + +-SEQAN_DIR = SeqAn-1.1 +-SEQAN_INC = -I $(SEQAN_DIR) +-INC = $(SEQAN_INC) -I third_party ++INC = `pkg-config --cflags seqan-1.4` + CPP = g++ + CXX = $(CPP) + CC = gcc +@@ -168,7 +166,6 @@ + $(wildcard genomes/NC_008253.fna) \ + $(wildcard reads/e_coli_1000.*) \ + $(wildcard reads/e_coli_1000_*) \ +- SeqAn-1.1 \ + bowtie \ + bowtie-build \ + bowtie-inspect \ diff --git a/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch b/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch new file mode 100644 index 000000000000..cd2a67b6a52b --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch @@ -0,0 +1,29 @@ +Fix building with C++14, which errors out due to differing semantics between C++98 +and C++14 with regards to allowing destructors to throw exceptions. +See also: https://bugs.gentoo.org/show_bug.cgi?id=593966 + +--- a/blockwise_sa.h ++++ b/blockwise_sa.h +@@ -87,7 +87,11 @@ + _logger(__logger) + { } + +- virtual ~BlockwiseSA() { } ++ virtual ~BlockwiseSA() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif ++ { } + + /** + * Get the next suffix; compute the next bucket if necessary. +@@ -216,6 +220,9 @@ + { _randomSrc.init(__seed); reset(); } + + ~KarkkainenBlockwiseSA() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif + { + #ifdef WITH_TBB + tbb_grp.wait(); diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml new file mode 100644 index 000000000000..71e8d3bb8e0f --- /dev/null +++ b/sci-biology/bowtie/metadata.xml @@ -0,0 +1,16 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + + bowtie-bio + + + Enables building bowtie with the Intel + Threading Building Blocks from dev-cpp/tbb. This + flag is recommended. + + -- cgit v1.2.3