From 87fe60fe4fbe65c67f68c60cae54ebac5c76fcdc Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 2 Jun 2010 11:37:10 +0000
Subject: [PATCH] Fix for Sendu. new Process and p.waitFor() don't seem to work
 on his farm. Throws an IOException. This was a problem way back with
 AnalyzeCovariates too.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3469 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../variantrecalibration/GenerateVariantClustersWalker.java  | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

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 dcb2a7388..4b1af125f 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
@@ -224,10 +224,7 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
 
             // Execute the RScript command to plot the table of truth values
             try {
-                final Process p = Runtime.getRuntime().exec( rScriptCommandLine );
-                p.waitFor();
-            } catch (InterruptedException e) {
-                throw new StingException(e.getMessage());
+                Runtime.getRuntime().exec( rScriptCommandLine );
             } catch ( IOException e ) {
                 throw new StingException( "Unable to execute RScript command: " + rScriptCommandLine );
             }