commit: 77a54a4d9f64ce2bfff0ef2928500cefd5cb1b9d Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Wed Mar 17 10:37:01 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Wed Mar 17 10:37:01 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=77a54a4d
sci-biology/bowtie: add version 1.3.0 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> sci-biology/bowtie/bowtie-1.3.0.ebuild | 63 ++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) diff --git a/sci-biology/bowtie/bowtie-1.3.0.ebuild b/sci-biology/bowtie/bowtie-1.3.0.ebuild new file mode 100644 index 000000000..118cc1303 --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.3.0.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/"; +SRC_URI="https://github.com/BenLangmead/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="Artistic" +SLOT="1" +KEYWORDS="~amd64 ~x86" + +IUSE="examples +tbb" + +RDEPEND="tbb? ( dev-cpp/tbb )" +DEPEND="${RDEPEND} + app-arch/unzip" +# sci-biology/seqan:1.4" + +DOCS=( AUTHORS NEWS TUTORIAL doc/README ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +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 +}
