| # Copyright 1999-2015 Gentoo Foundation |
| # Distributed under the terms of the GNU General Public License v2 |
| # $Id$ |
| |
| # TODO: |
| # -Fix javadoc generation OutOfMemoryError |
| # -Add launchers for 2 apps in biojava-apps.jar |
| # -Decide on demo packaging. (Whether to install its jar as done or sources by examples USE flag) |
| |
| EAPI=2 |
| |
| #JAVA_PKG_IUSE="doc source test" |
| JAVA_PKG_IUSE="source test" |
| |
| inherit eutils java-pkg-2 java-ant-2 |
| |
| DESCRIPTION="A Java framework for processing biological data" |
| HOMEPAGE="http://biojava.org" |
| SRC_URI="http://www.biojava.org/download/bj17/all/${P}-all.jar" |
| LICENSE="LGPL-2.1" |
| SLOT="0" |
| KEYWORDS="~amd64 ~x86" |
| IUSE="" |
| |
| COMMON_DEPEND="dev-java/jgrapht:0 |
| dev-java/commons-cli:1 |
| dev-java/commons-dbcp:0 |
| dev-java/commons-pool:0 |
| dev-java/commons-collections:0 |
| dev-java/bytecode:0" |
| |
| RDEPEND=">=virtual/jre-1.5 |
| ${COMMON_DEPEND}" |
| DEPEND=">=virtual/jdk-1.5 |
| app-arch/unzip |
| ${COMMON_DEPEND} |
| test? |
| ( |
| dev-java/junit:4 |
| dev-java/ant-junit4 |
| )" |
| |
| S="${WORKDIR}/biojava-${PV}" |
| |
| JAVA_ANT_IGNORE_SYSTEM_CLASSES="true" |
| |
| src_prepare() { |
| einfo "Removing bundled jars..." |
| find . -name "*.jar" -print -delete |
| java-pkg_jar-from jgrapht jgrapht.jar jgrapht-jdk1.5.jar |
| java-pkg_jar-from commons-cli-1 |
| java-pkg_jar-from commons-dbcp commons-dbcp.jar commons-dbcp-1.1.jar |
| java-pkg_jar-from commons-pool commons-pool.jar commons-pool-1.1.jar |
| java-pkg_jar-from bytecode |
| } |
| |
| src_compile() { |
| #ANT_OPTS="${ANT_OPTS} -Xmx512m" |
| eant package-biojava package-biojava package-demos package-apps #$(use_doc javadocs-all) |
| } |
| |
| src_install() { |
| java-pkg_newjar ant-build/biojava.jar ${PN}.jar |
| java-pkg_newjar ant-build/apps.jar ${PN}-apps.jar |
| java-pkg_newjar ant-build/demos.jar ${PN}-demos.jar |
| #use doc && java-pkg_dojavadoc ant-build/doc/{biojava,apps,demos} |
| use source && java-pkg_dosrc {src,apps,demos}/org |
| } |
| |
| src_test() { |
| java-pkg_jar-from junit-4 junit.jar junit-4.4.jar |
| ANT_TASKS="ant-junit4" eant runtests |
| } |
