commit: c9b8497a77f3a72c025ca02d8fd8bdb024e34189 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Apr 10 09:47:56 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Apr 10 09:48:08 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c9b8497a
sci-biology/bowtie: Version bump to 2.2.8 * EAPI=6 Package-Manager: portage-2.2.28 sci-biology/bowtie/Manifest | 1 + sci-biology/bowtie/bowtie-2.2.8.ebuild | 61 ++++++++++++++++++++++++++++++++++ 2 files changed, 62 insertions(+) diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest index 1291400..c41c821 100644 --- a/sci-biology/bowtie/Manifest +++ b/sci-biology/bowtie/Manifest @@ -1,2 +1,3 @@ DIST bowtie-1.1.2-src.zip 7713258 SHA256 b1e9ccc825207efd1893d9e33244c681bcb89b9b2b811eb95a9f5a92eab637ae SHA512 3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8 WHIRLPOOL 08cb824bf7a1ddfbe6692de67191aacf44776d7d4e0ab66bd2a13ecfffd087bc28cdde4c7285c781fa4759de0a239e68f87b702bcc2e24c9b81fda5804360ce7 DIST bowtie2-2.2.6-source.zip 5728779 SHA256 1000e90cdd90c3ca43c69d0d0ad951e190d36a6981a546f430a90ce86d64bfc8 SHA512 3ab5a5475cf214affd91e0d1782fd2d6dedccd979e3c809b5dfb272726d99ff1c7b59d92e387b187a7c2e43557786a1085186ccb96588de91212caf2eb94ce4f WHIRLPOOL 4fb02b3a0d76bbee0fe9abf91a71405922568bc38e593d5740df6279bad6f8b668df0debb0a81f3d3c23623558f34d842dd662a6838cf2d7f0fc8945fd00a298 +DIST bowtie2-2.2.8-source.zip 5734037 SHA256 4a36edf62c761082da1f7e7fcf363ec4ce022bd5e7c76dd3ab63fa6f0137c05b SHA512 be059498a6cb0d422b4cb0734c2067e55c66659d1e708c540d937aa52c967fc13081757fb44b8d42967b44ac6768fb00ad31fac63d69d09f2dcfd49cf4cffd62 WHIRLPOOL 6e980cc4b09280894572ffe5897387d8b414bb190a77fa53ecbae168a40dcc23afa2eee34da043e77c8e8c2d00b2da562c7d5d4a3dd7e440f8b88655b6fe56cb diff --git a/sci-biology/bowtie/bowtie-2.2.8.ebuild b/sci-biology/bowtie/bowtie-2.2.8.ebuild new file mode 100644 index 0000000..6e66420 --- /dev/null +++ b/sci-biology/bowtie/bowtie-2.2.8.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit eutils toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"; +SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" + +LICENSE="GPL-3" +SLOT="2" +KEYWORDS="~amd64 ~x86" + +IUSE="examples cpu_flags_x86_sse2 +tbb" + +RDEPEND="dev-lang/perl + tbb? ( dev-cpp/tbb )" +DEPEND="${RDEPEND} + app-arch/unzip" + +S="${WORKDIR}/${PN}2-${PV}" + +DOCS=( AUTHORS NEWS TUTORIAL ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +pkg_pretend() { + if ! use cpu_flags_x86_sse2 ; then + eerror "This package requires a CPU supporting the SSE2 instruction set." + die "SSE2 support missing" + fi +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CXX="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS} -msse2" \ + WITH_TBB="$(usex tbb 1 0)" +} + +src_install() { + dobin ${PN}2 ${PN}2-* + + exeinto /usr/libexec/${PN}2 + doexe scripts/* + + newman MANUAL ${PN}2.1 + einstalldocs + + if use examples; then + insinto /usr/share/${PN}2 + doins -r example + fi +}
