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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
This commit is contained in:
rpoplin 2010-06-02 11:37:10 +00:00
parent 7f0c638653
commit 87fe60fe4f
1 changed files with 1 additions and 4 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
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@ -224,10 +224,7 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
// Execute the RScript command to plot the table of truth values // Execute the RScript command to plot the table of truth values
try { try {
final Process p = Runtime.getRuntime().exec( rScriptCommandLine ); Runtime.getRuntime().exec( rScriptCommandLine );
p.waitFor();
} catch (InterruptedException e) {
throw new StingException(e.getMessage());
} catch ( IOException e ) { } catch ( IOException e ) {
throw new StingException( "Unable to execute RScript command: " + rScriptCommandLine ); throw new StingException( "Unable to execute RScript command: " + rScriptCommandLine );
} }