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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
This commit is contained in:
ebanks 2010-08-04 13:08:15 +00:00
parent 17d5e89734
commit 40ffe34686
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
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@ -37,6 +37,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList; import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import java.io.IOException; import java.io.IOException;
@ -243,7 +244,7 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
try { try {
Runtime.getRuntime().exec( rScriptCommandLine ); Runtime.getRuntime().exec( rScriptCommandLine );
} catch ( IOException e ) { } 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.");
} }
} }
} }