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commit: 94465f706e18530fe400311e03ae114e59a679af |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Thu Jun 30 21:19:52 2016 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Thu Jun 30 21:19:52 2016 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=94465f70 |
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|
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sci-biology/kraken: new package with huge requirements |
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|
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Package-Manager: portage-2.2.28 |
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|
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sci-biology/kraken/kraken-0.10.5.ebuild | 55 +++++++++++++++++++++++++++++++++ |
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sci-biology/kraken/metadata.xml | 12 +++++++ |
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2 files changed, 67 insertions(+) |
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|
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diff --git a/sci-biology/kraken/kraken-0.10.5.ebuild b/sci-biology/kraken/kraken-0.10.5.ebuild |
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new file mode 100644 |
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index 0000000..540c73d |
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--- /dev/null |
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+++ b/sci-biology/kraken/kraken-0.10.5.ebuild |
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@@ -0,0 +1,55 @@ |
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+# Copyright 1999-2016 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $Id$ |
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+ |
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+EAPI=5 |
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+ |
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+PERL_EXPORT_PHASE_FUNCTIONS=no |
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+inherit perl-module |
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+ |
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+DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups" |
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+HOMEPAGE="http://ccb.jhu.edu/software/kraken |
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+ http://genomebiology.com/2014/15/3/R46" |
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+SRC_URI="http://ccb.jhu.edu/software/kraken/dl/kraken-0.10.5-beta.tgz |
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+ http://ccb.jhu.edu/software/kraken/MANUAL.html" |
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+ |
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+LICENSE="GPL-3" |
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+SLOT="0" |
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+KEYWORDS="~amd64" |
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+IUSE="" |
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+ |
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+DEPEND="" |
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+RDEPEND="${DEPEND} |
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+ dev-lang/perl |
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+ net-misc/wget" |
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+ |
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+S="${WORKDIR}"/kraken-0.10.5-beta |
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+ |
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+src_prepare(){ |
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+ sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i src/Makefile || die |
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+ echo "exit 0" >> install_kraken.sh || die |
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+} |
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+ |
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+src_compile(){ |
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+ ./install_kraken.sh destdir || die |
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+} |
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+ |
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+src_install(){ |
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+ dohtml "${DISTDIR}"/MANUAL.html |
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+ perl_set_version |
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+ insinto ${VENDOR_LIB}/${PN} |
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+ doins destdir/*.pm |
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+ insinto /usr/share/${PN}/util |
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+ doins destdir/*.pl |
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+ chmod -R a+rx "${D}"/"${EPREFIX}"/usr/share/${PN}/util |
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+ rm -f destdir/krakenlib.pm |
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+ dobin destdir/* |
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+} |
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+ |
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+pkg_postinst(){ |
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+ ewarn "Kraken may optionally need <=sci-biology/jellyfish-2 if you want to build your own dbs" |
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+ ewarn "Kraken needs high network bandwidth for its huge downloads, be sure to read" |
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+ ewarn "http://ccb.jhu.edu/software/kraken and prepare at least 160GB of disk space" |
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+ ewarn "Consider placing the db files in ramfs (needs root permissions) taking >75GB RAM" |
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+ ewarn "Results can be visualized with http://sourceforge.net/p/krona/home/krona" |
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+} |
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|
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diff --git a/sci-biology/kraken/metadata.xml b/sci-biology/kraken/metadata.xml |
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new file mode 100644 |
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index 0000000..f68a1b6 |
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--- /dev/null |
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+++ b/sci-biology/kraken/metadata.xml |
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@@ -0,0 +1,12 @@ |
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+<?xml version="1.0" encoding="UTF-8"?> |
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+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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+<pkgmetadata> |
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+ <maintainer type="person"> |
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+ <email>mmokrejs@×××××××××××××××.cz</email> |
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+ <name>Martin Mokrejs</name> |
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+ </maintainer> |
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+ <maintainer type="project"> |
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+ <email>sci-biology@g.o</email> |
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+ <name>Gentoo Biology Project</name> |
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+ </maintainer> |
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+</pkgmetadata> |