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| author |   David Seifert <soap@gentoo.org> | 2016-04-09 20:26:28 +0200 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2016-04-09 20:57:05 +0200 |
| commit | 1e3f5d88f730c5d04b64095114d2e48c1ec4ba58 (patch) | |
| tree | f067251bfa8ccc7481541eb1a5cab6b955fc9172 /sci-biology/bowtie/bowtie-1.1.2-r1.ebuild | |
| parent | sci-biology/seqan: SLOT 1.4 and 2.1, allow for parallel installation (diff) | |
| download | gentoo-1e3f5d88f730c5d04b64095114d2e48c1ec4ba58.tar.gz gentoo-1e3f5d88f730c5d04b64095114d2e48c1ec4ba58.tar.bz2 gentoo-1e3f5d88f730c5d04b64095114d2e48c1ec4ba58.zip | |
sci-biology/bowtie: unbundle SeqAn, import Debian patches
* EAPI=6
Package-Manager: portage-2.2.28
Diffstat (limited to 'sci-biology/bowtie/bowtie-1.1.2-r1.ebuild')
| -rw-r--r-- | sci-biology/bowtie/bowtie-1.1.2-r1.ebuild | 75 |
1 files changed, 75 insertions, 0 deletions
diff --git a/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild b/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild new file mode 100644 index 000000000000..e0b435899caa --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild @@ -0,0 +1,75 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +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 +} |