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# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=5
inherit java-pkg-2
# download 134MB in size!
DESCRIPTION="CGView Comparison Tool to compare genome sequences graphically (aka CCT)"
HOMEPAGE="http://stothard.afns.ualberta.ca/downloads/CCT"
SRC_URI="http://www.ualberta.ca/~stothard/downloads/cgview_comparison_tool.zip"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64"
IUSE=""
DEPEND=">=dev-lang/perl-5.8.8
>=sci-biology/ncbi-tools-2.2.15
>=virtual/jre-1.4.2
dev-java/xerces
dev-java/batik
dev-java/commons-lang
>=media-gfx/imagemagick-6
>=sci-biology/bioperl-1.4.0"
RDEPEND="${DEPEND}"
S="${WORKDIR}"/cgview_comparison_tool
src_install() {
echo 'CCT_HOME='${EPREFIX}'/usr/share/cgview_comparison_tool' > "${S}/99cgview"
echo 'PATH="$PATH":"'${CCT_HOME}'/scripts"' >> "${S}/99cgview"
doenvd "${S}/99cgview" || die
#export PATH="$PATH":"${CCT_HOME}/scripts":/path/to/blast-2.2.25/bin
#export PERL5LIB="${CCT_HOME}"/lib/bioperl-1.2.3:"${CCT_HOME}"/lib/perl_modules:"$PERL5LIB"
dobin bin/cgview.jar
}
src_test(){
./update_cogs.sh || die
./test.sh || die
}
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