From 1aceeb44d5163cf26d028e1483dbeed2d751f2e3 Mon Sep 17 00:00:00 2001
From: Andrey Kislyuk <kislyuk@onyx.(none)>
Date: Sat, 10 Oct 2009 06:33:42 -0400
Subject: New package, ebuild written by me

---
 sci-biology/jalview/ChangeLog          |  7 ++++
 sci-biology/jalview/Manifest           |  4 +++
 sci-biology/jalview/jalview-2.4.ebuild | 60 ++++++++++++++++++++++++++++++++++
 sci-biology/jalview/metadata.xml       |  9 +++++
 4 files changed, 80 insertions(+)
 create mode 100644 sci-biology/jalview/ChangeLog
 create mode 100644 sci-biology/jalview/Manifest
 create mode 100644 sci-biology/jalview/jalview-2.4.ebuild
 create mode 100644 sci-biology/jalview/metadata.xml

diff --git a/sci-biology/jalview/ChangeLog b/sci-biology/jalview/ChangeLog
new file mode 100644
index 000000000..d83140491
--- /dev/null
+++ b/sci-biology/jalview/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-biology/jalview
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  10 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
+  New package, ebuild written by me
+
diff --git a/sci-biology/jalview/Manifest b/sci-biology/jalview/Manifest
new file mode 100644
index 000000000..766297820
--- /dev/null
+++ b/sci-biology/jalview/Manifest
@@ -0,0 +1,4 @@
+DIST jalview_2_4.tar.gz 11319073 RMD160 770f57a9c9b7822c0b13d0dfa46977b95ad8384a SHA1 f0f69b3b4716285aece7fc914df3a3133baf1abe SHA256 c4fe3a4b214ed7f06d48bd88fd53e068c2151390ec8004acd6705bea47b4918a
+EBUILD jalview-2.4.ebuild 1764 RMD160 02ce95fe3152ab424609b3789e60669e23d62d5c SHA1 da36d1747192093277de48e8a85c84991c58ff6e SHA256 79b2fa96a1a1f0109393e7f54b2ada9d506084d5b4436a5a22af3f3e44a82c29
+MISC ChangeLog 218 RMD160 691cb6907bf3038353f64854d9842ba4bdab3682 SHA1 9db1dfeee42326b0ea72b26101a2ed764fe2d382 SHA256 ee59ea378bf4fa6067d3d594c433d1e7f7475d37b8f07fb4916b032b8c346457
+MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
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/*
+}
diff --git a/sci-biology/jalview/metadata.xml b/sci-biology/jalview/metadata.xml
new file mode 100644
index 000000000..3302123e5
--- /dev/null
+++ b/sci-biology/jalview/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>weaver@gentoo.org</email>
+		<name>Andrey Kislyuk</name>
+	</maintainer>
+	<herd>sci-biology</herd>
+</pkgmetadata>
-- 
cgit v1.2.3-65-gdbad