commit: bae149ca5806b0db04206b0569f733a6c41a1007 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sat Sep 24 11:24:04 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sat Sep 24 11:24:04 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=bae149ca
sci-biology/idba: new package, needed by biopieces, github issue #381 Package-Manager: portage-2.3.0 sci-biology/idba/idba-1.1.1.ebuild | 34 ++++++++++++++++++++++++++++++++++ sci-biology/idba/idba-9999.ebuild | 34 ++++++++++++++++++++++++++++++++++ sci-biology/idba/metadata.xml | 12 ++++++++++++ 3 files changed, 80 insertions(+) diff --git a/sci-biology/idba/idba-1.1.1.ebuild b/sci-biology/idba/idba-1.1.1.ebuild new file mode 100644 index 0000000..d3a82a5 --- /dev/null +++ b/sci-biology/idba/idba-1.1.1.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +DESCRIPTION="De novo De Bruijn graph assembler iteratively using multimple k-mers" +HOMEPAGE="http://i.cs.hku.hk/~alse/hkubrg/projects/idba + https://code.google.com/archive/p/hku-idba"; +SRC_URI="https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/hku-idba/${P}.tar.gz"; + +LICENSE="GPL-2+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +src_prepare(){ + # Makefile.am also forces '-fopenmp -pthread', do we care? + find . -name Makefile.in | while read f; do \ + sed -e 's/-Wall -O3//' -i $f || die + done || die + default +} + +src_install(){ + default + # https://github.com/loneknightpy/idba/issues/23 + rm "${D}"/usr/bin/scan.py "${D}"/usr/bin/run-unittest.py || die + rm bin/test bin/*.o bin/Makefile* || die # avoid file collision + dobin bin/* +} diff --git a/sci-biology/idba/idba-9999.ebuild b/sci-biology/idba/idba-9999.ebuild new file mode 100644 index 0000000..3252524 --- /dev/null +++ b/sci-biology/idba/idba-9999.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit git-r3 + +DESCRIPTION="De novo De Bruijn graph assembler iteratively using multimple k-mers" +HOMEPAGE="http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud"; +EGIT_REPO_URI="https://github.com/loneknightpy/idba.git"; + +LICENSE="GPL-2+" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +src_prepare(){ + find . -name Makefile.in | while read f; do \ + sed -e 's/-Wall -O3//' -i $f || die + done + default +} + +src_install(){ + default + # https://github.com/loneknightpy/idba/issues/23 + rm "${D}"/usr/bin/scan.py "${D}"/usr/bin/run-unittest.py || die + rm bin/test bin/*.o bin/Makefile* || die # avoid file collision + dobin bin/* +} diff --git a/sci-biology/idba/metadata.xml b/sci-biology/idba/metadata.xml new file mode 100644 index 0000000..f68a1b6 --- /dev/null +++ b/sci-biology/idba/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata>
