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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="Error correct PacBio subreads using Illumina reads"
HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread"
if [ "$PV" == "9999" ]; then
inherit git-r3
EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread"
else
SRC_URI="https://github.com/BioInf-Wuerzburg/${PN}/releases/download/${P}/${P}.tar.gz"
KEYWORDS="~amd64 ~x86"
fi
LICENSE="Artistic-2 GPL-3 blasr"
SLOT="0"
# TODO: package shrimp and update blasr
# blasr requires new dep libblasr, which
# I cannot get to compile successfully
RDEPEND="
>=dev-lang/perl-5.10
dev-perl/Log-Log4perl
dev-perl/File-Which
>=sci-biology/ncbi-tools++-2.2.24
>=sci-biology/samtools-1.1
"
DEPEND="${RDEPEND}"
src_install(){
cd bin || die
dobin ChimeraToSeqFilter.pl dazz2sam ccseq bam2cns test_cfg.pl siamaera samfilter sam2cns proovread-flex proovread
cd ../util/bwa || die
dobin bwa-proovread # xa2multi.pl qualfa2fq.pl libbwa.a bwa.1
cd ../../util/SeqFilter || die
dobin bin/SeqFilter
cd ../../util/SeqChunker || die
dobin bin/*
cd ../../lib || die
perl_domodule -r -C ${PN} *
cd ../util/blasr-1.3.1 || die
dobin blasr
}
pkg_postinst(){
einfo "Proovread uses its own, modified version of bwa as bwa-proovread"
einfo "with linked in libbwa.a. It also bundles shrimp2 and blasr"
}
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