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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=5
USE_RUBY="ruby19 ruby20"
inherit ruby-fakegem
DESCRIPTION="Variant analysis tools (true SNPs, insertions, deletions) from whole exome capture sequencing (WECS)"
HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas2"
SRC_URI="http://downloads.sourceforge.net/project/atlas2/Atlas2_v1.4.3.zip"
LICENSE="BSD"
SLOT="0"
KEYWORDS=""
IUSE=""
DEPEND="
sci-biology/samtools
sci-biology/blat
sci-biology/phrap
sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, aka Jim Kent's src
RDEPEND="${DEPEND}"
S="${WORKDIR}"/all/"${PN}"_v"${PV}"
src_compile(){
cd SOLiD-SNP-caller || die
emake
cd ../vcfPrinter
# TODO: install the *.rb files
cd ../Atlas-Indel2
# TODO: install the *.rb and files in lib/
cd ../Atlas-SNP2
# TODO: install
}
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