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Diffstat (limited to 'sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild')
-rw-r--r-- | sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild | 81 |
1 files changed, 81 insertions, 0 deletions
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 +} |