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commit: 85794dc2e25580c628e007d4a528ffc2e24d4239 |
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Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Tue Feb 19 11:20:51 2019 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Tue Feb 19 11:20:51 2019 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=85794dc2 |
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|
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sci-biology/bowtie: working 1.2.2 snapshot |
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|
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This ebuild keeps the bundled SeqAn-1.1 sources (a library of |
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headers) and does not insist on system-wide installed |
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SeqAn-1.4 (for which too many patches are needed and I am unable |
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to evaluate/apply them all). |
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|
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Package-Manager: Portage-2.3.61, Repoman-2.3.12 |
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Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz> |
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|
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.../bowtie/bowtie-1.2.2_beta20190219.ebuild | 81 ++++++++++++++++++++++ |
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sci-biology/bowtie/bowtie-9999.ebuild | 81 ++++++++++++++++++++++ |
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.../files/bowtie-1.2.2-fix-isa-return-type.patch | 22 ++++++ |
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3 files changed, 184 insertions(+) |
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|
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diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild |
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new file mode 100644 |
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index 000000000..fcf0b4516 |
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--- /dev/null |
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+++ b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild |
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@@ -0,0 +1,81 @@ |
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+# Copyright 1999-2019 Gentoo Authors |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=6 |
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+ |
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+inherit flag-o-matic toolchain-funcs git-r3 |
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+ |
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+DESCRIPTION="Popular short read aligner for Next-generation sequencing data" |
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+HOMEPAGE="http://bowtie-bio.sourceforge.net/" |
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+EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git" |
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+EGIT_BRANCH="bug_fixes" |
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+COMMIT="f253e204f5ba4565d14ae1b300ea6cb10dfe4660" |
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+ |
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+LICENSE="Artistic" |
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+SLOT="1" |
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+KEYWORDS="~amd64 ~x86" |
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+ |
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+IUSE="examples +tbb" |
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+ |
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+RDEPEND="tbb? ( dev-cpp/tbb )" |
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+DEPEND="${RDEPEND} |
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+ app-arch/unzip" |
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+# sci-biology/seqan:1.4" |
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+ |
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+DOCS=( AUTHORS NEWS TUTORIAL doc/README ) |
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+HTML_DOCS=( doc/{manual.html,style.css} ) |
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+ |
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+PATCHES=( "${FILESDIR}/bowtie-1.2.2-fix-isa-return-type.patch" ) |
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+# not needed |
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+# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b |
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+# |
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+# still to be considered |
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+#PATCHES=( |
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+# "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" |
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+# "${FILESDIR}/${P}-unbundle-seqan.patch" |
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+# "${FILESDIR}/${P}-fix-setBegin-call.patch" |
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+# "${FILESDIR}/${P}-seqan-popcount.patch" |
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+# "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch" |
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+# "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch" |
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+# "${FILESDIR}/${P}-spelling.patch" |
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+# "${FILESDIR}/${P}-tbb-tinythread-missing.patch" |
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+#) |
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+ |
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+src_prepare() { |
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+ default |
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+ |
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+ # remove bundled library of headers, use system seqan 1.4 |
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+ # rm -rf SeqAn-1.1/ third_party/ || die |
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+ |
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+ # innocuous non-security flags, prevent log pollution |
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+ append-cxxflags \ |
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+ -Wno-unused-local-typedefs \ |
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+ -Wno-unused-but-set-variable \ |
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+ -Wno-unused-variable |
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+} |
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+ |
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+src_compile() { |
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+ emake \ |
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+ CC="$(tc-getCC)" \ |
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+ CPP="$(tc-getCXX)" \ |
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+ CFLAGS="" \ |
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+ CXXFLAGS="" \ |
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+ EXTRA_FLAGS="${LDFLAGS}" \ |
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+ RELEASE_FLAGS="${CXXFLAGS}" \ |
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+ WITH_TBB="$(usex tbb 1 0)" |
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+} |
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+ |
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+src_install() { |
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+ dobin ${PN} ${PN}-* |
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+ |
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+ exeinto /usr/libexec/${PN} |
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+ doexe scripts/* |
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+ |
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+ newman MANUAL ${PN}.1 |
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+ einstalldocs |
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+ |
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+ if use examples; then |
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+ insinto /usr/share/${PN} |
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+ doins -r genomes indexes |
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+ fi |
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+} |
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|
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diff --git a/sci-biology/bowtie/bowtie-9999.ebuild b/sci-biology/bowtie/bowtie-9999.ebuild |
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new file mode 100644 |
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index 000000000..d54d0a544 |
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--- /dev/null |
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+++ b/sci-biology/bowtie/bowtie-9999.ebuild |
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@@ -0,0 +1,81 @@ |
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+# Copyright 1999-2019 Gentoo Authors |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=6 |
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+ |
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+inherit flag-o-matic toolchain-funcs git-r3 |
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+ |
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+DESCRIPTION="Popular short read aligner for Next-generation sequencing data" |
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+HOMEPAGE="http://bowtie-bio.sourceforge.net/" |
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+EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git" |
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+EGIT_BRANCH="bug_fixes" |
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+ |
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+LICENSE="Artistic" |
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+SLOT="1" |
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+KEYWORDS="" |
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+ |
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+IUSE="examples +tbb" |
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+ |
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+RDEPEND="tbb? ( dev-cpp/tbb )" |
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+DEPEND="${RDEPEND} |
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+ sci-biology/seqan:1.4 |
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+ app-arch/unzip" |
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+ |
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+DOCS=( AUTHORS NEWS TUTORIAL doc/README ) |
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+HTML_DOCS=( doc/{manual.html,style.css} ) |
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+ |
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+PATCHES=( "${FILESDIR}/bowtie-9999-fix-isa-return-type.patch" ) |
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+# not needed |
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+# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b |
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+#PATCHES=( |
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+# "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" |
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+# "${FILESDIR}/${P}-fix-Intel-compilation.patch" |
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+# "${FILESDIR}/${P}-unbundle-seqan.patch" |
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+#) |
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+# other patches to be still considered |
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+# "${FILESDIR}/${P}-fix-setBegin-call.patch" |
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+# "${FILESDIR}/${P}-seqan-popcount.patch" |
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+# "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch" |
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+# "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch" |
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+# "${FILESDIR}/${P}-spelling.patch" |
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+# "${FILESDIR}/${P}-tbb-tinythread-missing.patch" |
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+#) |
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+ |
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+src_prepare() { |
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+ default |
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+ |
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+ # remove bundled libraries, use system seqan 1.4 |
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+ # rm -rf SeqAn-1.1/ third_party/ || die |
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+ |
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+ # innocuous non-security flags, prevent log pollution |
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+ append-cxxflags \ |
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+ -Wno-unused-local-typedefs \ |
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+ -Wno-unused-but-set-variable \ |
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+ -Wno-unused-variable |
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+} |
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+ |
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+src_compile() { |
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+ emake \ |
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+ CC="$(tc-getCC)" \ |
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+ CPP="$(tc-getCXX)" \ |
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+ CFLAGS="" \ |
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+ CXXFLAGS="" \ |
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+ EXTRA_FLAGS="${LDFLAGS}" \ |
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+ RELEASE_FLAGS="${CXXFLAGS}" \ |
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+ WITH_TBB="$(usex tbb 1 0)" |
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+} |
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+ |
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+src_install() { |
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+ dobin ${PN} ${PN}-* |
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+ |
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+ exeinto /usr/libexec/${PN} |
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+ doexe scripts/* |
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+ |
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+ newman MANUAL ${PN}.1 |
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+ einstalldocs |
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+ |
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+ if use examples; then |
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+ insinto /usr/share/${PN} |
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+ doins -r genomes indexes |
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+ fi |
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+} |
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|
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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 |
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new file mode 100644 |
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index 000000000..de19e42a8 |
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--- /dev/null |
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+++ b/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch |
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@@ -0,0 +1,22 @@ |
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+From 58c6ac97b1938909881877ef83167f5eff0e8ab1 Mon Sep 17 00:00:00 2001 |
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+From: Rone Charles <rone_charles@××××××××.com> |
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+Date: Tue, 4 Sep 2018 21:06:39 -0400 |
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+Subject: [PATCH] Fix isa return type |
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+ |
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+--- |
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+ ebwt.h | 2 +- |
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+ 1 file changed, 1 insertion(+), 1 deletion(-) |
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+ |
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+diff --git a/ebwt.h b/ebwt.h |
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+index fe6300cc..8f886b8d 100644 |
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+--- a/ebwt.h |
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++++ b/ebwt.h |
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+@@ -862,7 +862,7 @@ class Ebwt { |
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+ TIndexOffU* ftab() const { return _ftab; } |
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+ TIndexOffU* eftab() const { return _eftab; } |
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+ TIndexOffU* offs() const { return _offs; } |
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+- uint32_t* isa() const { return _isa; } /* check */ |
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++ TIndexOffU* isa() const { return _isa; } /* check */ |
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+ TIndexOffU* plen() const { return _plen; } |
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+ TIndexOffU* rstarts() const { return _rstarts; } |
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+ uint8_t* ebwt() const { return _ebwt; } |