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-rw-r--r--biology/jalview/files/jalview.sh.in3
-rw-r--r--biology/jalview/files/patch-build.xml50
2 files changed, 1 insertions, 52 deletions
diff --git a/biology/jalview/files/jalview.sh.in b/biology/jalview/files/jalview.sh.in
index 33b1a7e75195..eb25b886f2de 100644
--- a/biology/jalview/files/jalview.sh.in
+++ b/biology/jalview/files/jalview.sh.in
@@ -1,4 +1,3 @@
#!/bin/sh
-# Shell script to launch jalview using our javavm wrapper
-"%%LOCALBASE%%/bin/java" -Djava.ext.dirs="%%DATADIR%%" -cp "%%DATADIR%%/jalview.jar" jalview.bin.Jalview
+%%JAVA%% -classpath %%DATADIR%% -jar %%DATADIR%%/jalview.jar jalview.bin.Jalview
diff --git a/biology/jalview/files/patch-build.xml b/biology/jalview/files/patch-build.xml
deleted file mode 100644
index 7d6449347ba4..000000000000
--- a/biology/jalview/files/patch-build.xml
+++ /dev/null
@@ -1,50 +0,0 @@
-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">