commit: 94465f706e18530fe400311e03ae114e59a679af Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Thu Jun 30 21:19:52 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu Jun 30 21:19:52 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=94465f70
sci-biology/kraken: new package with huge requirements Package-Manager: portage-2.2.28 sci-biology/kraken/kraken-0.10.5.ebuild | 55 +++++++++++++++++++++++++++++++++ sci-biology/kraken/metadata.xml | 12 +++++++ 2 files changed, 67 insertions(+) diff --git a/sci-biology/kraken/kraken-0.10.5.ebuild b/sci-biology/kraken/kraken-0.10.5.ebuild new file mode 100644 index 0000000..540c73d --- /dev/null +++ b/sci-biology/kraken/kraken-0.10.5.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module + +DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups" +HOMEPAGE="http://ccb.jhu.edu/software/kraken + http://genomebiology.com/2014/15/3/R46"; +SRC_URI="http://ccb.jhu.edu/software/kraken/dl/kraken-0.10.5-beta.tgz + http://ccb.jhu.edu/software/kraken/MANUAL.html"; + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + dev-lang/perl + net-misc/wget" + +S="${WORKDIR}"/kraken-0.10.5-beta + +src_prepare(){ + sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i src/Makefile || die + echo "exit 0" >> install_kraken.sh || die +} + +src_compile(){ + ./install_kraken.sh destdir || die +} + +src_install(){ + dohtml "${DISTDIR}"/MANUAL.html + perl_set_version + insinto ${VENDOR_LIB}/${PN} + doins destdir/*.pm + insinto /usr/share/${PN}/util + doins destdir/*.pl + chmod -R a+rx "${D}"/"${EPREFIX}"/usr/share/${PN}/util + rm -f destdir/krakenlib.pm + dobin destdir/* +} + +pkg_postinst(){ + ewarn "Kraken may optionally need <=sci-biology/jellyfish-2 if you want to build your own dbs" + ewarn "Kraken needs high network bandwidth for its huge downloads, be sure to read" + ewarn "http://ccb.jhu.edu/software/kraken and prepare at least 160GB of disk space" + ewarn "Consider placing the db files in ramfs (needs root permissions) taking >75GB RAM" + ewarn "Results can be visualized with http://sourceforge.net/p/krona/home/krona"; +} diff --git a/sci-biology/kraken/metadata.xml b/sci-biology/kraken/metadata.xml new file mode 100644 index 0000000..f68a1b6 --- /dev/null +++ b/sci-biology/kraken/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>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata>
