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# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=3
inherit java-pkg-2 java-ant-2
[ "$PV" == "9999" ] && inherit git-2
DESCRIPTION="DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool"
HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"
if [ "$PV" == "9999" ]; then
EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis"
KEYWORDS="~amd64 ~x86"
else
SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/v13/v"${PV}"/artemis_compiled_v"${PV}".tar.gz"
KEYWORDS="~amd64 ~x86"
fi
LICENSE="GPL-2"
SLOT="0"
KEYWORDS=""
IUSE=""
# uses its own BamView
DEPEND="sci-biology/samtools
>=virtual/jdk-1.5
>=dev-java/sun-jdk-1.5
dev-java/ant-core"
RDEPEND="${DEPEND}
>=virtual/jre-1.5"
# http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00551.html
# http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00561.html
# http://gmod.org/wiki/Artemis-Chado_Integration_Tutorial
src_compile() {
emake || die
# ant compile || die
einfo "Need to figure out where does the GeneBuilder application come from so that one could use Chado for automated gene prediction pipeline"
}
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