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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
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"
}
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