2 files changed, 59 insertions, 0 deletions
diff --git a/biology/jalview/files/jalview.sh.in b/biology/jalview/files/jalview.sh.in
new file mode 100644
index 000000000000..0444e47656ea
--- /dev/null
+++ b/biology/jalview/files/jalview.sh.in
@@ -0,0 +1,7 @@
+#!/bin/sh
+#
+# $FreeBSD$
+
+# Shell script to launch jalview using our javavm wrapper
+
+JAVA_VERSION="%%JAVA_VERSION%%" "%%LOCALBASE%%/bin/java" -Djava.ext.dirs="%%DATADIR%%" -cp "%%DATADIR%%/jalview.jar" jalview.bin.Jalview
diff --git a/biology/jalview/files/patch-build.xml b/biology/jalview/files/patch-build.xml
new file mode 100644
index 000000000000..d7cd9ab4a814
--- /dev/null
+++ b/biology/jalview/files/patch-build.xml
@@ -0,0 +1,52 @@
+$FreeBSD$
+
+This patch removes the webstart support.
+
+--- build.xml.orig	Mon Dec 12 14:57:02 2005
++++ build.xml	Fri Jan 27 12:20:52 2006
+@@ -180,6 +180,10 @@
+         </fileset>
+       </copy>
+ <!-- the default keystore details might need to be edited here -->
++<!-- Remove all the remaining stuff for this target 
++     which is only necessary if we want to start jalview
++     using java web start. It requires us to generate a key 
++     before building the port - Fernan - 27.Jan.2006 
+       <signjar
+       storepass="alignmentisfun"
+       keypass="alignmentisfun"
+@@ -194,8 +198,9 @@
+       </fileset>
+       </signjar>
+       <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
+-
++-->
+       <!--    codebase="http://www.jalview.org/jalview/webstart" -->
++<!--
+       <jnlp toFile="${packageDir}/jalview.jnlp" href="jalview.jnlp"
+       codebase="${WebStartLocation}">
+       <information>
+@@ -206,6 +211,7 @@
+         <description kind="short">Jalview</description>
+         <icon href="logo_big.gif"/>
+         <offline_allowed/>
++-->
+ 	<!--
+ 	<association mime-type="application-x/ext-file" extensions="fa"/>
+         <association mime-type="application-x/ext-file" extensions="fasta"/>
+@@ -216,6 +222,7 @@
+         <association mime-type="application-x/ext-file" extensions="aln"/>
+         <association mime-type="application-x/ext-file" extensions="pir"/>
+ 	-->
++<!--
+        </information>
+         <resources>
+           <j2se version="1.4+"/>
+@@ -234,6 +241,7 @@
+           <all_permissions/>
+         </security>
+       </jnlp>
++-->
+     </target>
+     <target name="runenv" depends="init">
+       <path id="run.classpath">