From 40ffe34686386786ed04a8dc70976b51d8f0733d Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 4 Aug 2010 13:08:15 +0000
Subject: [PATCH] Warn user instead of dying if the R script cannot be executed

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3928 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../variantrecalibration/GenerateVariantClustersWalker.java    | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
index 7a7343ebf..01fbe897c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
@@ -37,6 +37,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.commandline.Argument;
 
 import java.io.IOException;
@@ -243,7 +244,7 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
             try {
                 Runtime.getRuntime().exec( rScriptCommandLine );
             } catch ( IOException e ) {
-                throw new StingException( "Unable to execute RScript command: " + rScriptCommandLine );
+                Utils.warnUser("Unable to execute the RScript command.  While not critical to the calculations themselves, the script outputs a report that is extremely useful for confirming that the recalibration proceded as expected.  We highly recommend trying to rerun the script manually if possible.");
             }
         }
     }