commit: 841b73539cdc92799497752d37b764c16793582b Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Tue Mar 16 18:11:02 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Tue Mar 16 18:11:02 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=841b7353
Revert "sci-biology/bowtie: drop old" This reverts commit 718c86792641e4203877c23d69e9d4dcb0274388. Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> .../bowtie/bowtie-1.2.2_beta20190219.ebuild | 81 ++++++++++++++++++++++ .../files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch | 17 +++++ .../files/bowtie-1.2.2-fix-Intel-compilation.patch | 32 +++++++++ .../files/bowtie-1.2.2-fix-isa-return-type.patch | 22 ++++++ .../bowtie/files/bowtie-1.2.2-unbundle-seqan.patch | 14 ++++ .../bowtie/files/bowtie-1.2.2-void2int.patch | 16 +++++ 6 files changed, 182 insertions(+) diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild new file mode 100644 index 000000000..f7a1b92d4 --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic toolchain-funcs git-r3 + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/"; +EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git"; +EGIT_BRANCH="bug_fixes" +COMMIT="f253e204f5ba4565d14ae1b300ea6cb10dfe4660" + +LICENSE="Artistic" +SLOT="1" +KEYWORDS="~amd64 ~x86" + +IUSE="examples +tbb" + +RDEPEND="tbb? ( dev-cpp/tbb )" +DEPEND="${RDEPEND} + app-arch/unzip" +# sci-biology/seqan:1.4" + +DOCS=( AUTHORS NEWS TUTORIAL doc/README ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +PATCHES=( "${FILESDIR}/bowtie-1.2.2-fix-isa-return-type.patch" ) +# not needed +# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b +# +# still to be considered +#PATCHES=( +# "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" +# "${FILESDIR}/${P}-unbundle-seqan.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" +#) + +src_prepare() { + default + + # remove bundled library of headers, 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/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch b/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch new file mode 100644 index 000000000..4bcd61ba3 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.2.2-_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 <gw.foss...@gmail.com> +Last-Update: 2014-100-06 + +--- bowtie-1.2.2/diff_sample.h 2017-11-03 01:25:56.000000000 +0100 ++++ bowtie-1.2.2/diff_sample.h 2019-02-18 12:50:37.894674282 +0100 +@@ -979,7 +979,7 @@ + { + Timer timer(cout, " Invoking Larsson-Sadakane on ranks time: ", this->verbose()); + VMSG_NL(" Invoking Larsson-Sadakane on ranks"); +- _Context_LSS<TIndexOff> c; ++ ContextLss_<TIndexOff> c; + c.suffixsort( + (TIndexOff*)begin(_isaPrime, Standard()), + (TIndexOff*)begin(sPrime, Standard()), diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch b/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch new file mode 100644 index 000000000..75942efb5 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch @@ -0,0 +1,32 @@ +fix compilation errors with Intel compilers: +error: no operator "=" matches these operands +author: Ward Poelmans +--- bowtie-1.2.2/hit.h 2018-01-24 12:57:47.135575442 +0100 ++++ bowtie-1.2.2/hit.h 2018-01-24 12:57:58.615869774 +0100 +@@ -640,10 +640,26 @@ + s.moveTo(btString); + } + ++ batch(const batch &other) ++ { ++ batchId = other.batchId; ++ isWritten = other.isWritten; ++ btString = other.btString; ++ } ++ + bool operator<(const batch& other) const { + return batchId < other.batchId; + } + ++ batch& operator=(batch&& other) { ++ if (&other != this) { ++ batchId = other.batchId; ++ isWritten = other.isWritten; ++ other.btString.moveTo(btString); ++ } ++ return *this; ++ } ++ + batch& operator=(batch& other) { + if (&other != this) { + batchId = other.batchId; diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch b/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch new file mode 100644 index 000000000..de19e42a8 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch @@ -0,0 +1,22 @@ +From 58c6ac97b1938909881877ef83167f5eff0e8ab1 Mon Sep 17 00:00:00 2001 +From: Rone Charles <rone_char...@fastmail.com> +Date: Tue, 4 Sep 2018 21:06:39 -0400 +Subject: [PATCH] Fix isa return type + +--- + ebwt.h | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/ebwt.h b/ebwt.h +index fe6300cc..8f886b8d 100644 +--- a/ebwt.h ++++ b/ebwt.h +@@ -862,7 +862,7 @@ class Ebwt { + TIndexOffU* ftab() const { return _ftab; } + TIndexOffU* eftab() const { return _eftab; } + TIndexOffU* offs() const { return _offs; } +- uint32_t* isa() const { return _isa; } /* check */ ++ TIndexOffU* isa() const { return _isa; } /* check */ + TIndexOffU* plen() const { return _plen; } + TIndexOffU* rstarts() const { return _rstarts; } + uint8_t* ebwt() const { return _ebwt; } diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch b/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch new file mode 100644 index 000000000..b1a5f98f5 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch @@ -0,0 +1,14 @@ +--- bowtie-1.2.2/Makefile 2019-02-18 13:26:29.490835084 +0100 ++++ bowtie-1.2.2/Makefile 2019-02-18 13:28:36.864742545 +0100 +@@ -5,10 +5,7 @@ + prefix = /usr/local + bindir = $(prefix)/bin + +-SEQAN_DIR = ./SeqAn-1.1 +-# treat SeqAn as a sysdir to suppress warnings +-SEQAN_INC = -isystem $(SEQAN_DIR) +-INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party ++INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) `pkg-config --cflags seqan-1.4` -I third_party + CPP = g++ + CXX = $(CPP) + CC = gcc diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch b/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch new file mode 100644 index 000000000..822b673ae --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch @@ -0,0 +1,16 @@ +#The latest Intel compiler (2016,2017) complains about the incompatibility of "void *" argument +#being incompatible with parameter of type "int *" +#M. Fujinaga (fujin...@ualberta.ca) +--- processor_support.h 2017-02-02 21:48:42.436432756 +0000 ++++ processor_support.h 2017-02-02 21:48:54.419309743 +0000 +@@ -44,8 +44,8 @@ + + try { + #if ( defined(USING_INTEL_COMPILER) || defined(USING_MSC_COMPILER) ) +- __cpuid((void *) ®s,0); // test if __cpuid() works, if not catch the exception +- __cpuid((void *) ®s,0x1); // POPCNT bit is bit 23 in ECX ++ __cpuid((int *) ®s,0); // test if __cpuid() works, if not catch the exception ++ __cpuid((int *) ®s,0x1); // POPCNT bit is bit 23 in ECX + #elif defined(USING_GCC_COMPILER) + __get_cpuid(0x1, ®s.EAX, ®s.EBX, ®s.ECX, ®s.EDX); + #else
