From b2e699169cf1c545e92db2536be2cab656c472fe Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Wed, 28 Nov 2012 15:26:05 -0500
Subject: [PATCH] Update GATK packaging settings to package arbitrary resources

With the newly-added support for packaging arbitrary resources, the
resources were getting packaged in a normal build but not when
creating a standalone GATK jar. This corrects this oversight.
---
 public/packages/GATKEngine.xml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/public/packages/GATKEngine.xml b/public/packages/GATKEngine.xml
index 2de0273f3..d0b4a52b5 100644
--- a/public/packages/GATKEngine.xml
+++ b/public/packages/GATKEngine.xml
@@ -36,6 +36,9 @@
       <dir name="org/broadinstitute/sting/utils/R" includes="**/*.tar.gz" />
       <!-- All R scripts in org.broadinstitute.sting -->
       <dir name="org/broadinstitute/sting" includes="**/*.R" />
+      <!-- Resources in org.broadinstitute.sting -->
+      <dir name="org/broadinstitute/sting" includes="**/resources/*" />
+      <dir name="org/broadinstitute/sting" includes="**/templates/*" />
       <!-- The GATK public key -->
       <file path="GATK_public.key" />
     </dependencies>