1 files changed, 60 insertions, 0 deletions
diff --git a/sci-biology/jalview/jalview-2.4.ebuild b/sci-biology/jalview/jalview-2.4.ebuild
new file mode 100644
index 000000000..d1c1dea85
--- /dev/null
+++ b/sci-biology/jalview/jalview-2.4.ebuild
@@ -0,0 +1,60 @@
+# 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/*
+}