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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit java-pkg-2 java-ant-2 git-r3
DESCRIPTION="DNA sequence viewer/annotation (Artemis) and comparison (ACT) tool"
HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"
SRC_URI="
ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf -> ${P}.manual.pdf
ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/art_html_build.zip -> ${P}.html_build.zip"
EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS=""
IUSE=""
# uses its own BamView
RDEPEND="
sci-biology/samtools:0
>=virtual/jre-1.6:*"
DEPEND="${RDEPEND}
!sci-biology/artemis-bin
dev-java/ant-core
>=virtual/jdk-1.6:*
dev-java/log4j
dev-java/jdbc-postgresql
dev-java/jakarta-regexp
dev-java/batik
dev-java/j2ssh
sci-biology/picard
dev-java/biojava"
# some more dependencies extracted from /usr/bin/act
# JacORB.jar, jemAlign.jar, macos.jar, chado-14-interface.jar, iBatis, biojava.jar,
#
# 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
# BamView is at http://bamview.sourceforge.net/
src_unpack(){
unzip "${DISTDIR}"/art_html_build.zip || die
}
src_compile(){
ant || die
}
src_install(){
dobin act act.command art dnaplotter gff2embl
java-pkg_dojar ant-build/artemis.jar
dodoc "${DISTDIR}"/"${P}".manual.pdf README
insinto /usr/share/doc/"${PN}"/html
doins art_html_build/*
}
# artemis_compiled_v16.0.11.tar.gz contains compiled binaries but also java *.class files
# artemis_v16.0.11.jar and sartemis_v16.0.11.jar
# ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/v16.0.11/
pkg_postinst(){
einfo "For BAM file support please install sci-biology/BamView"
einfo "You may find interesting the additional web resources:"
einfo "http://www.webact.org/WebACT"
einfo "http://www.hpa-bioinfotools.org.uk/pise/double_act.html"
}
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