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# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
inherit perl-functions
DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups"
HOMEPAGE="https://ccb.jhu.edu/software/kraken"
SRC_URI="https://github.com/DerrickWood/kraken/archive/v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-3"
SLOT="1"
KEYWORDS="~amd64"
DEPEND=""
RDEPEND="${DEPEND}
dev-lang/perl
net-misc/wget
sci-biology/jellyfish:1
"
src_prepare(){
default
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(){
dodoc -r docs
perl_set_version
perl_domodule destdir/*.pm
dosym ../../"${VENDOR_LIB//${EPREFIX/}}/krakenlib.pm" /usr/bin/krakenlib.pm
insinto /usr/share/${PN}/util
doins destdir/*.pl
chmod -R a+rx "${ED}/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 "https://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 https://sourceforge.net/p/krona/home/krona"
}
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