commit: 85794dc2e25580c628e007d4a528ffc2e24d4239 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Tue Feb 19 11:20:51 2019 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Tue Feb 19 11:20:51 2019 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=85794dc2
sci-biology/bowtie: working 1.2.2 snapshot This ebuild keeps the bundled SeqAn-1.1 sources (a library of headers) and does not insist on system-wide installed SeqAn-1.4 (for which too many patches are needed and I am unable to evaluate/apply them all). Package-Manager: Portage-2.3.61, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz> .../bowtie/bowtie-1.2.2_beta20190219.ebuild | 81 ++++++++++++++++++++++ sci-biology/bowtie/bowtie-9999.ebuild | 81 ++++++++++++++++++++++ .../files/bowtie-1.2.2-fix-isa-return-type.patch | 22 ++++++ 3 files changed, 184 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..fcf0b4516 --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2019 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/bowtie-9999.ebuild b/sci-biology/bowtie/bowtie-9999.ebuild new file mode 100644 index 000000000..d54d0a544 --- /dev/null +++ b/sci-biology/bowtie/bowtie-9999.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2019 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" + +LICENSE="Artistic" +SLOT="1" +KEYWORDS="" + +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}/bowtie-9999-fix-isa-return-type.patch" ) +# not needed +# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b +#PATCHES=( +# "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" +# "${FILESDIR}/${P}-fix-Intel-compilation.patch" +# "${FILESDIR}/${P}-unbundle-seqan.patch" +#) +# other patches to be still considered +# "${FILESDIR}/${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 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/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 <[email protected]> +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; }
