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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
inherit java-pkg-2
PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module eutils toolchain-funcs
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=""
IUSE=""
DEPEND="
>=dev-lang/perl-5.8.8
>=sci-biology/ncbi-tools-2.2.15
>=virtual/jre-1.4.2:*
dev-java/xerces:2
dev-java/batik
dev-java/commons-lang:2.1
>=media-gfx/imagemagick-6
>=sci-biology/bioperl-1.4.0"
RDEPEND="${DEPEND}"
S="${WORKDIR}"/cgview_comparison_tool
src_test(){
./update_cogs.sh || die
./test.sh || die
}
src_install() {
insinto /usr/share/${PN}/scripts
chmod a+x scripts/* # BUG: this does not work
doins scripts/*
echo 'CCT_HOME='${EPREFIX}'/usr/share/cgview' > "${S}/99cgview"
echo 'PATH="$PATH":"'${CCT_HOME}'/scripts"' >> "${S}/99cgview"
doenvd "${S}/99cgview"
perl_set_version
insinto ${VENDOR_LIB}/cgview
doins lib/perl_modules/Util/*.pm
#
# Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/batik/svggen/SVGGraphics2DIOException
java-pkg_dojar bin/cgview.jar
}
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