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# Copyright 1999-2009 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/beast-mcmc/beast-mcmc-1.5.1.ebuild,v 1.1 2009/10/02 21:47:11 weaver Exp $
EAPI="2"
EANT_GENTOO_CLASSPATH="jmol,castor-1.0,log4j,commons-logging,commons-discovery,wsdl4j,xerces-2,saaj,vecmath,javahelp,sun-jaf"
JAVA_ANT_REWRITE_CLASSPATH="true"
EANT_BUILD_TARGET="distclean makedist"
JAVA_PKG_IUSE="source doc"
inherit java-pkg-2 java-ant-2 eutils
DESCRIPTION="A multiple DNA sequence alignment editor"
HOMEPAGE="http://www.jalview.org/"
SRC_URI="http://www.jalview.org/source/jalview_2_4.tar.gz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
COMMON_DEPS=">=sci-chemistry/jmol-11.0.2 <sci-chemistry/jmol-11.1
dev-java/castor:1.0
dev-java/log4j"
DEPEND=">=virtual/jdk-1.5
${COMMON_DEPS}"
RDEPEND=">=virtual/jre-1.5
dev-java/commons-discovery
dev-java/commons-logging
dev-java/saaj
dev-java/xerces
dev-java/wsdl4j
dev-java/vecmath
dev-java/javahelp
dev-java/sun-jaf
dev-java/sun-javamail
${COMMON_DEPS}"
S="${WORKDIR}/${PN}"
java_prepare() {
perl -i -ne'print unless /<jalopy/../<\/jalopy>/ or /<taskdef.+name="jalopy"/../<\/taskdef>/ or /<include name="jalview-jalopy.xml"/' build.xml
find -name '*.jar' | egrep -v '(vamsas|axis|jaxrpc|roxes-ant-tasks|regex|xml-apis)' | xargs rm -v
}
src_install() {
java-pkg_dojar dist/*.jar
MY_CP=""
for i in $(cd dist; ls *.jar); do
MY_CP="${MY_CP}:${ROOT}usr/share/${PN}/lib/$i"
done
java-pkg_dolauncher jalview --main jalview.bin.Jalview \
--java_args "-cp ${MY_CP}:$(java-config -p ${EANT_GENTOO_CLASSPATH})"
use source && java-pkg_dosrc src
# use doc && java-pkg_dojavadoc something - no docs to be seen
dodoc README doc/*
}
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