No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.

Other minor cleanup.

build.xml

@@ -38,6 +38,7 @@
     <property name="java.private.source.dir" value="${private.dir}/java/src" />
     <property name="java.classes" value="${build.dir}/java/classes" />
     <property name="R.public.scripts.dir" value="${public.dir}/R/scripts" />
+    <property name="R.private.scripts.dir" value="${private.dir}/R/scripts" />
     <property name="R.public.src.dir" value="${public.dir}/R/src" />
     <!-- Legacy: Installing libraries back into the source directory
     instead of the build or dist directory... intentionally avoids ant clean?? -->
@@ -571,6 +572,9 @@
             <fileset dir="${R.public.scripts.dir}">
               <include name="**/utils/**/*.R"/>
             </fileset>
+            <fileset dir="${R.private.scripts.dir}" erroronmissingdir="false">
+              <include name="**/utils/**/*.R"/>
+            </fileset>
             <manifest>
                 <attribute name="Premain-Class" value="org.broadinstitute.sting.utils.instrumentation.Sizeof" />
             </manifest>
@@ -603,6 +607,10 @@
                 <include name="**/gatk/**/*.R"/>
                 <include name="**/alignment/**/*.R"/>
             </fileset>
+            <fileset dir="${R.private.scripts.dir}" erroronmissingdir="false">
+                <include name="**/gatk/**/*.R"/>
+                <include name="**/alignment/**/*.R"/>
+            </fileset>
             <manifest>
                 <attribute name="Main-Class" value="org.broadinstitute.sting.gatk.CommandLineGATK" />
             </manifest>
@@ -621,6 +629,10 @@
                 <include name="**/analyzecovariates/**/*.R"/>
                 <include name="**/gatk/walkers/recalibration/**/*.R"/>
             </fileset>
+            <fileset dir="${R.private.scripts.dir}" erroronmissingdir="false">
+                <include name="**/analyzecovariates/**/*.R"/>
+                <include name="**/gatk/walkers/recalibration/**/*.R"/>
+            </fileset>
           <manifest>
             <attribute name="Main-Class" value="org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates" />
           </manifest>
@@ -653,6 +665,9 @@
             <fileset dir="${R.public.scripts.dir}">
                 <include name="org/broadinstitute/sting/queue/**/*.R"/>
             </fileset>
+            <fileset dir="${R.private.scripts.dir}" erroronmissingdir="false">
+                <include name="org/broadinstitute/sting/queue/**/*.R"/>
+            </fileset>
             <manifest>
                 <attribute name="Main-Class" value="org.broadinstitute.sting.queue.QCommandLine" />
             </manifest>
@@ -842,6 +857,7 @@
         <pathelement location="${scala.private.test.classes}" />
         <pathelement location="${R.tar.dir}" />
         <pathelement location="${R.public.scripts.dir}" />
+        <pathelement location="${R.private.scripts.dir}" />
     </path>
 
     <path id="testng.gatk.releasetest.classpath">

public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java

@@ -25,6 +25,9 @@
 
 package org.broadinstitute.sting.analyzecovariates;
 
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
@@ -33,14 +36,16 @@ import org.broadinstitute.sting.gatk.walkers.recalibration.Covariate;
 import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum;
 import org.broadinstitute.sting.gatk.walkers.recalibration.RecalibrationArgumentCollection;
 import org.broadinstitute.sting.utils.R.RScriptExecutor;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.sting.utils.io.Resource;
 import org.broadinstitute.sting.utils.text.XReadLines;
 
 import java.io.*;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.Collection;
 import java.util.Map;
 import java.util.regex.Pattern;
@@ -71,15 +76,13 @@ import java.util.regex.Pattern;
  * </ul>
  *
  * <p>
- * NOTE: For those running this tool externally from the Broad, it is crucial to note that both the -Rscript and -resources options
+ * NOTE: Rscript needs to be in your environment PATH (this is the scripting version of R, not the interactive version).
- * must be changed from the default. -Rscript needs to point to your installation of Rscript (this is the scripting version of R,
+ * See <a target="r-project" href="http://www.r-project.org">http://www.r-project.org</a> for more info on how to download and install R.
- * not the interactive version) while -resources needs to point to the folder holding the R scripts that are used. For those using
- * this tool as part of the Binary Distribution the -resources should point to the resources folder that is part of the tarball.
- * For those using this tool by building from the git repository the -resources should point to the R/ subdirectory of the Sting checkout.
  *
  * <p>
  * See the GATK wiki for a tutorial and example recalibration accuracy plots.
- * http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration
+ * <a target="gatkwiki" href="http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration"
+ * >http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration</a>
  *
  * <h2>Input</h2>
  * <p>
@@ -91,7 +94,6 @@ import java.util.regex.Pattern;
  * java -Xmx4g -jar AnalyzeCovariates.jar \
  *   -recalFile /path/to/recal.table.csv  \
  *   -outputDir /path/to/output_dir/  \
- *   -resources resources/  \
  *   -ignoreQ 5
  * </pre>
  *
@@ -101,6 +103,11 @@ import java.util.regex.Pattern;
         groupName = "AnalyzeCovariates",
         summary = "Package to plot residual accuracy versus error covariates for the base quality score recalibrator")
 public class AnalyzeCovariates extends CommandLineProgram {
+    final private static Logger logger = Logger.getLogger(AnalyzeCovariates.class);
+
+    private static final String PLOT_RESDIUAL_ERROR_QUALITY_SCORE_COVARIATE = "plot_residualError_QualityScoreCovariate.R";
+    private static final String PLOT_RESDIUAL_ERROR_OTHER_COVARIATE = "plot_residualError_OtherCovariate.R";
+    private static final String PLOT_INDEL_QUALITY_RSCRIPT = "plot_indelQuality.R";
 
     /////////////////////////////
     // Command Line Arguments
@@ -114,11 +121,7 @@ public class AnalyzeCovariates extends CommandLineProgram {
     @Input(fullName = "recal_file", shortName = "recalFile", doc = "The input recal csv file to analyze", required = false)
     private String RECAL_FILE = "output.recal_data.csv";
     @Argument(fullName = "output_dir", shortName = "outputDir", doc = "The directory in which to output all the plots and intermediate data files", required = false)
-    private String OUTPUT_DIR = "analyzeCovariates/";
+    private File OUTPUT_DIR = new File("analyzeCovariates");
-    @Argument(fullName = "path_to_Rscript", shortName = "Rscript", doc = "The path to your implementation of Rscript. For Broad users this is maybe /broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.12.0/bin/Rscript", required = false)
-    private String PATH_TO_RSCRIPT = "Rscript";
-    @Argument(fullName = "path_to_resources", shortName = "resources", doc = "Path to resources folder holding the Sting R scripts.", required = false)
-    private String PATH_TO_RESOURCES = "public/R/";
     @Argument(fullName = "ignoreQ", shortName = "ignoreQ", doc = "Ignore bases with reported quality less than this number.", required = false)
     private int IGNORE_QSCORES_LESS_THAN = 5;
     @Argument(fullName = "numRG", shortName = "numRG", doc = "Only process N read groups. Default value: -1 (process all read groups)", required = false)
@@ -154,29 +157,26 @@ public class AnalyzeCovariates extends CommandLineProgram {
     protected int execute() {
 
         // create the output directory where all the data tables and plots will go
-        try {
+        if (!OUTPUT_DIR.exists() && !OUTPUT_DIR.mkdirs())
-            Process p = Runtime.getRuntime().exec("mkdir " + OUTPUT_DIR);
+            throw new UserException.BadArgumentValue("--output_dir/-outDir", "Unable to create output directory: " + OUTPUT_DIR);
-        } catch (IOException e) {
+
-            System.out.println("Couldn't create directory: " + OUTPUT_DIR);
+        if (!RScriptExecutor.RSCRIPT_EXISTS)
-            System.out.println("User is responsible for making sure the output directory exists.");
+            Utils.warnUser(logger, "Rscript not found in environment path. Plots will not be generated.");
-        }
-        if( !OUTPUT_DIR.endsWith("/") ) { OUTPUT_DIR = OUTPUT_DIR + "/"; }
-        if( !PATH_TO_RESOURCES.endsWith("/") ) { PATH_TO_RESOURCES = PATH_TO_RESOURCES + "/"; }
 
         // initialize all the data from the csv file and allocate the list of covariates
-        System.out.println("Reading in input csv file...");
+        logger.info("Reading in input csv file...");
         initializeData();
-        System.out.println("...Done!");
+        logger.info("...Done!");
 
         // output data tables for Rscript to read in
-        System.out.println("Writing out intermediate tables for R...");
+        logger.info("Writing out intermediate tables for R...");
         writeDataTables();
-        System.out.println("...Done!");
+        logger.info("...Done!");
 
         // perform the analysis using Rscript and output the plots
-        System.out.println("Calling analysis R scripts and writing out figures...");
+        logger.info("Calling analysis R scripts and writing out figures...");
         callRScripts();
-        System.out.println("...Done!");
+        logger.info("...Done!");
 
         return 0;
     }
@@ -287,37 +287,40 @@ public class AnalyzeCovariates extends CommandLineProgram {
             if(NUM_READ_GROUPS_TO_PROCESS == -1 || ++numReadGroups <= NUM_READ_GROUPS_TO_PROCESS) {
                 String readGroup = readGroupKey.toString();
                 RecalDatum readGroupDatum = (RecalDatum) dataManager.getCollapsedTable(0).data.get(readGroupKey);
-                System.out.print("Writing out data tables for read group: " + readGroup + "\twith " + readGroupDatum.getNumObservations() + " observations"  );
+                logger.info(String.format(
-                System.out.println("\tand aggregate residual error = " + String.format("%.3f", readGroupDatum.empiricalQualDouble(0, MAX_QUALITY_SCORE) - readGroupDatum.getEstimatedQReported()));
+                        "Writing out data tables for read group: %s\twith %s observations\tand aggregate residual error = %.3f",
+                        readGroup, readGroupDatum.getNumObservations(),
+                        readGroupDatum.empiricalQualDouble(0, MAX_QUALITY_SCORE) - readGroupDatum.getEstimatedQReported()));
 
                 // for each covariate
                 for( int iii = 1; iii < requestedCovariates.size(); iii++ ) {
                     Covariate cov = requestedCovariates.get(iii);
 
                     // Create a PrintStream
-                    PrintStream output = null;
+                    File outputFile = new File(OUTPUT_DIR, readGroup + "." + cov.getClass().getSimpleName()+ ".dat");
+                    PrintStream output;
                     try {
-                        output = new PrintStream(new FileOutputStream(OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat"));
+                        output = new PrintStream(FileUtils.openOutputStream(outputFile));
-
+                    } catch (IOException e) {
-                    } catch (FileNotFoundException e) {
+                        throw new UserException.CouldNotCreateOutputFile(outputFile, e);
-                        System.err.println("Can't create file: " + OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat");
-                        System.exit(-1);
                     }
 
-                    // Output the header
+                    try {
-                    output.println("Covariate\tQreported\tQempirical\tnMismatches\tnBases");
+                        // Output the header
+                        output.println("Covariate\tQreported\tQempirical\tnMismatches\tnBases");
 
-                    for( Object covariateKey : ((Map)dataManager.getCollapsedTable(iii).data.get(readGroupKey)).keySet()) {
+                        for( Object covariateKey : ((Map)dataManager.getCollapsedTable(iii).data.get(readGroupKey)).keySet()) {
-                        output.print( covariateKey.toString() + "\t" );                                                     // Covariate
+                            output.print( covariateKey.toString() + "\t" );                                                     // Covariate
-                        RecalDatum thisDatum = (RecalDatum)((Map)dataManager.getCollapsedTable(iii).data.get(readGroupKey)).get(covariateKey);
+                            RecalDatum thisDatum = (RecalDatum)((Map)dataManager.getCollapsedTable(iii).data.get(readGroupKey)).get(covariateKey);
-                        output.print( String.format("%.3f", thisDatum.getEstimatedQReported()) + "\t" );                    // Qreported
+                            output.print( String.format("%.3f", thisDatum.getEstimatedQReported()) + "\t" );                    // Qreported
-                        output.print( String.format("%.3f", thisDatum.empiricalQualDouble(0, MAX_QUALITY_SCORE)) + "\t" );  // Qempirical
+                            output.print( String.format("%.3f", thisDatum.empiricalQualDouble(0, MAX_QUALITY_SCORE)) + "\t" );  // Qempirical
-                        output.print( thisDatum.getNumMismatches() + "\t" );                                                // nMismatches
+                            output.print( thisDatum.getNumMismatches() + "\t" );                                                // nMismatches
-                        output.println( thisDatum.getNumObservations() );                                                   // nBases
+                            output.println( thisDatum.getNumObservations() );                                                   // nBases
+                        }
+                    } finally {
+                        // Close the PrintStream
+                        IOUtils.closeQuietly(output);
                     }
-
-                    // Close the PrintStream
-                    output.close();
                 }
             } else {
                 break;
@@ -327,10 +330,6 @@ public class AnalyzeCovariates extends CommandLineProgram {
     }
 
     private void callRScripts() {
-        RScriptExecutor.RScriptArgumentCollection argumentCollection =
-                new RScriptExecutor.RScriptArgumentCollection(PATH_TO_RSCRIPT, Arrays.asList(PATH_TO_RESOURCES));
-        RScriptExecutor executor = new RScriptExecutor(argumentCollection, true);
-
         int numReadGroups = 0;
 
         // for each read group
@@ -338,23 +337,32 @@ public class AnalyzeCovariates extends CommandLineProgram {
             if(++numReadGroups <= NUM_READ_GROUPS_TO_PROCESS || NUM_READ_GROUPS_TO_PROCESS == -1) {
 
                 String readGroup = readGroupKey.toString();
-                System.out.println("Analyzing read group: " + readGroup);
+                logger.info("Analyzing read group: " + readGroup);
 
                 // for each covariate
                 for( int iii = 1; iii < requestedCovariates.size(); iii++ ) {
                     Covariate cov = requestedCovariates.get(iii);
-                    final String outputFilename = OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat";
+                    final File outputFile = new File(OUTPUT_DIR, readGroup + "." + cov.getClass().getSimpleName()+ ".dat");
                     if (DO_INDEL_QUALITY) {
-                        executor.callRScripts("plot_indelQuality.R", outputFilename,
+                        RScriptExecutor executor = new RScriptExecutor();
-                                cov.getClass().getSimpleName().split("Covariate")[0]); // The third argument is the name of the covariate in order to make the plots look nice
+                        executor.addScript(new Resource(PLOT_INDEL_QUALITY_RSCRIPT, AnalyzeCovariates.class));
+                        // The second argument is the name of the covariate in order to make the plots look nice
+                        executor.addArgs(outputFile, cov.getClass().getSimpleName().split("Covariate")[0]);
+                        executor.exec();
                     }   else {
                         if( iii == 1 ) {
                             // Analyze reported quality
-                            executor.callRScripts("plot_residualError_QualityScoreCovariate.R", outputFilename,
+                            RScriptExecutor executor = new RScriptExecutor();
-                                    IGNORE_QSCORES_LESS_THAN, MAX_QUALITY_SCORE, MAX_HISTOGRAM_VALUE); // The third argument is the Q scores that should be turned pink in the plot because they were ignored
+                            executor.addScript(new Resource(PLOT_RESDIUAL_ERROR_QUALITY_SCORE_COVARIATE, AnalyzeCovariates.class));
+                            // The second argument is the Q scores that should be turned pink in the plot because they were ignored
+                            executor.addArgs(outputFile, IGNORE_QSCORES_LESS_THAN, MAX_QUALITY_SCORE, MAX_HISTOGRAM_VALUE);
+                            executor.exec();
                         } else { // Analyze all other covariates
-                            executor.callRScripts("plot_residualError_OtherCovariate.R", outputFilename,
+                            RScriptExecutor executor = new RScriptExecutor();
-                                    cov.getClass().getSimpleName().split("Covariate")[0]); // The third argument is the name of the covariate in order to make the plots look nice
+                            executor.addScript(new Resource(PLOT_RESDIUAL_ERROR_OTHER_COVARIATE, AnalyzeCovariates.class));
+                            // The second argument is the name of the covariate in order to make the plots look nice
+                            executor.addArgs(outputFile, cov.getClass().getSimpleName().split("Covariate")[0]);
+                            executor.exec();
                         }
                     }
                 }

public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java

@@ -35,9 +35,11 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.sting.utils.R.RScriptExecutor;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.io.Resource;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
@@ -101,6 +103,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
 
     public static final String VQS_LOD_KEY = "VQSLOD"; // Log odds ratio of being a true variant versus being false under the trained gaussian mixture model
     public static final String CULPRIT_KEY = "culprit"; // The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out
+    private static final String PLOT_TRANCHES_RSCRIPT = "plot_Tranches.R";
 
     @ArgumentCollection private VariantRecalibratorArgumentCollection VRAC = new VariantRecalibratorArgumentCollection();
 
@@ -158,12 +161,8 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     private double[] TS_TRANCHES = new double[] {100.0, 99.9, 99.0, 90.0};
     @Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified the variant recalibrator will use variants even if the specified filter name is marked in the input VCF file", required=false)
     private String[] IGNORE_INPUT_FILTERS = null;
-    @Argument(fullName="path_to_Rscript", shortName = "Rscript", doc = "The path to your implementation of Rscript. For Broad users this is maybe /broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.12.0/bin/Rscript", required=false)
+    @Output(fullName="rscript_file", shortName="rscriptFile", doc="The output rscript file generated by the VQSR to aid in visualization of the input data and learned model", required=false)
-    private String PATH_TO_RSCRIPT = "Rscript";
+    private File RSCRIPT_FILE = null;
-    @Argument(fullName="rscript_file", shortName="rscriptFile", doc="The output rscript file generated by the VQSR to aid in visualization of the input data and learned model", required=false)
-    private String RSCRIPT_FILE = null;
-    @Argument(fullName = "path_to_resources", shortName = "resources", doc = "Path to resources folder holding the Sting R scripts.", required=false)
-    private String PATH_TO_RESOURCES = "public/R/";
     @Argument(fullName="ts_filter_level", shortName="ts_filter_level", doc="The truth sensitivity level at which to start filtering, used here to indicate filtered variants in the model reporting plots", required=false)
     private double TS_FILTER_LEVEL = 99.0;
 
@@ -192,9 +191,13 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     //---------------------------------------------------------------------------------------------------------------
 
     public void initialize() {
-        if( !PATH_TO_RESOURCES.endsWith("/") ) { PATH_TO_RESOURCES = PATH_TO_RESOURCES + "/"; }
         dataManager = new VariantDataManager( new ArrayList<String>(Arrays.asList(USE_ANNOTATIONS)), VRAC );
 
+        if (RSCRIPT_FILE != null && !RScriptExecutor.RSCRIPT_EXISTS)
+            Utils.warnUser(logger, String.format(
+                    "Rscript not found in environment path. %s will be generated but PDF plots will not.",
+                    RSCRIPT_FILE));
+
         if( IGNORE_INPUT_FILTERS != null ) {
             ignoreInputFilterSet.addAll( Arrays.asList(IGNORE_INPUT_FILTERS) );
         }
@@ -327,20 +330,13 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
             createVisualizationScript( dataManager.getRandomDataForPlotting( 6000 ), goodModel, badModel, lodCutoff );
         }
 
-        // Execute Rscript command to create the tranche plot
-        // Print out the command line to make it clear to the user what is being executed and how one might modify it
-        final String rScriptTranchesCommandLine = PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_Tranches.R" + " " + TRANCHES_FILE.getAbsolutePath() + " " + TARGET_TITV;
-        logger.info( "Executing: " + rScriptTranchesCommandLine );
-
         // Execute the RScript command to plot the table of truth values
-        try {
+        RScriptExecutor executor = new RScriptExecutor();
-            Process p;
+        executor.addScript(new Resource(PLOT_TRANCHES_RSCRIPT, VariantRecalibrator.class));
-            p = Runtime.getRuntime().exec( rScriptTranchesCommandLine );
+        executor.addArgs(TRANCHES_FILE.getAbsoluteFile(), TARGET_TITV);
-            p.waitFor();
+        // Print out the command line to make it clear to the user what is being executed and how one might modify it
-        } catch ( Exception e ) {
+        logger.info("Executing: " + executor.getApproximateCommandLine());
-            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.");
+        executor.exec();
-        }
-
     }
 
     private void createVisualizationScript( final ExpandingArrayList<VariantDatum> randomData, final GaussianMixtureModel goodModel, final GaussianMixtureModel badModel, final double lodCutoff ) {
@@ -348,15 +344,18 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         try {
             stream = new PrintStream(RSCRIPT_FILE);
         } catch( FileNotFoundException e ) {
-            throw new UserException.CouldNotCreateOutputFile(RSCRIPT_FILE, "", e);
+            throw new UserException.CouldNotCreateOutputFile(RSCRIPT_FILE, e);
         }
 
         // We make extensive use of the ggplot2 R library: http://had.co.nz/ggplot2/
         stream.println("library(ggplot2)");
+        // For compactPDF in R 2.13+
+        stream.println("library(tools)");
 
         createArrangeFunction( stream );
 
-        stream.println("pdf(\"" + RSCRIPT_FILE + ".pdf\")"); // Unfortunately this is a huge pdf file, BUGBUG: need to work on reducing the file size
+        stream.println("outputPDF <- \"" + RSCRIPT_FILE + ".pdf\"");
+        stream.println("pdf(outputPDF)"); // Unfortunately this is a huge pdf file, BUGBUG: need to work on reducing the file size
 
         for(int iii = 0; iii < USE_ANNOTATIONS.length; iii++) {
             for( int jjj = iii + 1; jjj < USE_ANNOTATIONS.length; jjj++) {
@@ -431,18 +430,17 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         }
         stream.println("dev.off()");
 
+        stream.println("if (exists(\"compactPDF\")) {");
+        stream.println("compactPDF(ouputPDF)");
+        stream.println("}");
+
         stream.close();
 
         // Execute Rscript command to generate the clustering plots
-        final String rScriptTranchesCommandLine = PATH_TO_RSCRIPT + " " +  RSCRIPT_FILE;
+        RScriptExecutor executor = new RScriptExecutor();
-        logger.info( "Executing: " + rScriptTranchesCommandLine );
+        executor.addScript(RSCRIPT_FILE);
-        try {
+        logger.info("Executing: " + executor.getApproximateCommandLine());
-            Process p;
+        executor.exec();
-            p = Runtime.getRuntime().exec( rScriptTranchesCommandLine );
-            p.waitFor();
-        } catch ( Exception e ) {
-            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 visualizing the recalibration results.  We highly recommend trying to rerun the script manually if possible.");
-        }
      }
 
     // The Arrange function is how we place the 4 model plots on one page

public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutor.java

@@ -27,8 +27,6 @@ package org.broadinstitute.sting.utils.R;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.commandline.Advanced;
-import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -36,48 +34,33 @@ import org.broadinstitute.sting.utils.io.IOUtils;
 import org.broadinstitute.sting.utils.io.Resource;
 import org.broadinstitute.sting.utils.runtime.ProcessController;
 import org.broadinstitute.sting.utils.runtime.ProcessSettings;
+import org.broadinstitute.sting.utils.runtime.RuntimeUtils;
 
 import java.io.File;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
 
 /**
  * Generic service for executing RScripts
  */
 public class RScriptExecutor {
+    private static final String RSCRIPT_BINARY = "Rscript";
+    private static final File RSCRIPT_PATH = RuntimeUtils.which(RSCRIPT_BINARY);
+    public static final boolean RSCRIPT_EXISTS = (RSCRIPT_PATH != null);
+    private static final String RSCRIPT_MISSING_MESSAGE = "Please add the Rscript directory to your environment ${PATH}";
+
     /**
      * our log
      */
     private static Logger logger = Logger.getLogger(RScriptExecutor.class);
 
-    public static class RScriptArgumentCollection {
+    private boolean exceptOnError = false;
-        @Advanced
-        @Argument(fullName = "path_to_Rscript", shortName = "Rscript", doc = "The path to your implementation of Rscript. Defaults Rscript meaning to use the first available on the environment PATH. For Broad users should 'use R-2.12' or later.", required = false)
-        public String PATH_TO_RSCRIPT = "Rscript";
-
-        @Advanced
-        @Argument(fullName = "path_to_Rresources", shortName = "Rresources", doc = "Path to resources folder holding the Sting R scripts.", required = false)
-        public List<String> PATH_TO_RESOURCES = Arrays.asList("public/R/", "private/R/");
-
-        public RScriptArgumentCollection() {}
-
-        /* For testing and convenience */
-        public RScriptArgumentCollection(final String PATH_TO_RSCRIPT, final List<String> PATH_TO_RESOURCES) {
-            this.PATH_TO_RSCRIPT = PATH_TO_RSCRIPT;
-            this.PATH_TO_RESOURCES = PATH_TO_RESOURCES;
-        }
-    }
-
-    private final RScriptArgumentCollection myArgs;
-    private final boolean exceptOnError;
     private final List<RScriptLibrary> libraries = new ArrayList<RScriptLibrary>();
     private final List<Resource> scriptResources = new ArrayList<Resource>();
     private final List<File> scriptFiles = new ArrayList<File>();
     private final List<String> args = new ArrayList<String>();
 
-    public RScriptExecutor(final RScriptArgumentCollection myArgs, final boolean exceptOnError) {
+    public void setExceptOnError(boolean exceptOnError) {
-        this.myArgs = myArgs;
         this.exceptOnError = exceptOnError;
     }
 
@@ -103,7 +86,27 @@ public class RScriptExecutor {
             this.args.add(arg.toString());
     }
 
-    public void exec() {
+    public String getApproximateCommandLine() {
+        StringBuilder command = new StringBuilder("Rscript");
+        for (Resource script: this.scriptResources)
+            command.append(" (resource)").append(script.getFullPath());
+        for (File script: this.scriptFiles)
+            command.append(" ").append(script.getAbsolutePath());
+        for (String arg: this.args)
+            command.append(" ").append(arg);
+        return command.toString();
+    }
+
+    public boolean exec() {
+        if (!RSCRIPT_EXISTS) {
+            if (exceptOnError) {
+                throw new UserException.CannotExecuteRScript(RSCRIPT_MISSING_MESSAGE);
+            } else {
+                logger.warn("Skipping: " + getApproximateCommandLine());
+                return false;
+            }
+        }
+
         List<File> tempFiles = new ArrayList<File>();
         try {
             File tempLibDir = IOUtils.tempDir("R.", ".lib");
@@ -126,7 +129,7 @@ public class RScriptExecutor {
                 expression.append(");");
 
                 for (RScriptLibrary library: this.libraries) {
-                    expression.append("require('").append(library.getLibraryName()).append("', lib.loc=tempLibDir);");
+                    expression.append("library('").append(library.getLibraryName()).append("', lib.loc=tempLibDir);");
                 }
             }
 
@@ -142,7 +145,7 @@ public class RScriptExecutor {
 
             String[] cmd = new String[this.args.size() + 3];
             int i = 0;
-            cmd[i++] = myArgs.PATH_TO_RSCRIPT;
+            cmd[i++] = RSCRIPT_BINARY;
             cmd[i++] = "-e";
             cmd[i++] = expression.toString();
             for (String arg: this.args)
@@ -156,52 +159,30 @@ public class RScriptExecutor {
 
             ProcessController controller = ProcessController.getThreadLocal();
 
-            logger.debug("Executing: " + Utils.join(" ", cmd));
+            if (logger.isDebugEnabled()) {
-            logger.debug("Result: " + controller.exec(processSettings).getExitValue());
+                logger.debug("Executing:");
+                for (String arg: cmd)
+                    logger.debug("  " + arg);
+            }
+            int exitValue = controller.exec(processSettings).getExitValue();
+            logger.debug("Result: " + exitValue);
 
+            if (exitValue != 0)
+                throw new RScriptExecutorException(
+                        "RScript exited with " + exitValue +
+                                (logger.isDebugEnabled() ? "" : ". Run with -l DEBUG for more info."));
+
+            return true;
         } catch (StingException e) {
-            generateException(e);
+            if (exceptOnError) {
+                throw e;
+            } else {
+                logger.warn(e.getMessage());
+                return false;
+            }
         } finally {
             for (File temp: tempFiles)
                 FileUtils.deleteQuietly(temp);
         }
     }
-
-    public void callRScripts(String scriptName, Object... scriptArgs) {
-        final File pathToScript = findScript(scriptName);
-        if (pathToScript == null) return; // we failed but shouldn't exception out
-        addScript(pathToScript);
-        addArgs(scriptArgs);
-        exec();
-    }
-
-    public File findScript(final String scriptName) {
-        for ( String pathToResource : myArgs.PATH_TO_RESOURCES ) {
-            final File f = new File(pathToResource + "/" + scriptName);
-            if ( f.exists() ) {
-                if ( f.canRead() )
-                    return f;
-                else
-                    generateException("Script exists but couldn't be read: " + scriptName);
-            }
-        }
-
-        generateException("Couldn't find script: " + scriptName + " in " + myArgs.PATH_TO_RESOURCES);
-        return null;
-    }
-
-    private void generateException(String msg) {
-        generateException(msg, null);
-    }
-
-    private void generateException(Throwable e) {
-        generateException("", e);
-    }
-
-    private void generateException(String msg, Throwable e) {
-        if ( exceptOnError )
-            throw new UserException(msg, e);
-        else
-            logger.warn(msg + (e == null ? "" : ":" + e.getMessage()));
-    }
 }

public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutorException.java

@@ -0,0 +1,33 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.R;
+
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+
+public class RScriptExecutorException extends ReviewedStingException {
+    public RScriptExecutorException(String msg) {
+        super(msg);
+    }
+}

public/java/src/org/broadinstitute/sting/utils/Utils.java

@@ -80,20 +80,24 @@ public class Utils {
     }
 
     public static void warnUser(final String msg) {
+        warnUser(logger, msg);
+    }
+    
+    public static void warnUser(final Logger logger, final String msg) {
         logger.warn(String.format("********************************************************************************"));
         logger.warn(String.format("* WARNING:"));
         logger.warn(String.format("*"));
-        prettyPrintWarningMessage(msg);
+        prettyPrintWarningMessage(logger, msg);
         logger.warn(String.format("********************************************************************************"));
     }
-    
 
     /**
      * pretty print the warning message supplied
      *
+     * @param logger logger for the message
      * @param message the message
      */
-    private static void prettyPrintWarningMessage(String message) {
+    private static void prettyPrintWarningMessage(Logger logger, String message) {
         StringBuilder builder = new StringBuilder(message);
         while (builder.length() > 70) {
             int space = builder.lastIndexOf(" ", 70);

public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java

@@ -237,6 +237,9 @@ public class UserException extends ReviewedStingException {
      }
 
     public static class CannotExecuteRScript extends UserException {
+        public CannotExecuteRScript(String message) {
+            super(String.format("Unable to execute RScript command: " + message));
+        }
         public CannotExecuteRScript(String message, Exception e) {
             super(String.format("Unable to execute RScript command: " + message), e);
         }

public/java/src/org/broadinstitute/sting/utils/io/IOUtils.java

@@ -90,6 +90,18 @@ public class IOUtils {
         }
     }
 
+    /**
+     * Writes content to a temp file and returns the path to the temporary file.
+     *
+     * @param content   to write.
+     * @param prefix    Prefix for the temp file.
+     * @param suffix    Suffix for the temp file.
+     * @return the path to the temp file.
+     */
+    public static File writeTempFile(String content, String prefix, String suffix) {
+        return writeTempFile(content, prefix, suffix, null);
+    }
+
     /**
      * Writes content to a temp file and returns the path to the temporary file.
      *

public/java/src/org/broadinstitute/sting/utils/io/Resource.java

@@ -24,6 +24,8 @@
 
 package org.broadinstitute.sting.utils.io;
 
+import java.io.File;
+
 /**
  * Stores a resource by path and a relative class.
  */
@@ -50,4 +52,15 @@ public class Resource {
     public String getPath() {
         return path;
     }
+
+    public String getFullPath() {
+        if (relativeClass == null)
+            return path;
+        if (new File(path).isAbsolute())
+            return path;
+        return String.format("%s%s%s",
+                relativeClass.getPackage().getName().replace('.', File.separatorChar),
+                File.separator,
+                path);
+    }
 }

public/java/src/org/broadinstitute/sting/utils/runtime/RuntimeUtils.java

@@ -0,0 +1,58 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.runtime;
+
+import org.apache.commons.lang.StringUtils;
+
+import java.io.File;
+
+public class RuntimeUtils {
+    public static final String[] PATHS;
+
+    static {
+        String path = System.getenv("PATH");
+        if (path == null)
+            path = System.getenv("path");
+        if (path == null) {
+            PATHS = new String[0];
+        } else {
+            PATHS = StringUtils.split(path, File.pathSeparatorChar);
+        }
+    }
+
+    /**
+     * Returns the path to an executable or null if it doesn't exist.
+     * @param executable Relative path
+     * @return The absolute file path.
+     */
+    public static File which(String executable) {
+        for (String path: PATHS) {
+            File file = new File(path, executable);
+            if (file.exists())
+                return file.getAbsoluteFile();
+        }
+        return null;
+    }
+}

public/java/test/org/broadinstitute/sting/utils/R/RScriptExecutorUnitTest.java

@@ -26,60 +26,84 @@ package org.broadinstitute.sting.utils.R;
 
 import org.apache.commons.io.FileUtils;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.io.IOUtils;
+import org.testng.Assert;
 import org.testng.annotations.Test;
 
 import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
 
 /**
  * Basic unit test for RScriptExecutor in reduced reads
  */
 public class RScriptExecutorUnitTest extends BaseTest {
-    final static String testrscript = "print(\"hello, world\")\n";
-    final static String publicRScript = "plot_Tranches.R";
 
-    // --------------------------------------------------------------------------------
+    private static final String HELLO_WORLD_SCRIPT = "print('hello, world')";
-    //
+    private static final String GSALIB_LOADED_SCRIPT = "if (!'package:gsalib' %in% search()) stop('gsalib not loaded')";
-    // Difference testing routines
-    //
-    // --------------------------------------------------------------------------------
-
-    private void testOne(String script, String pathToRscript, String anotherSearchPath, boolean exceptOnError) {
-        RScriptExecutor.RScriptArgumentCollection collection =
-                new RScriptExecutor.RScriptArgumentCollection();
-        if ( pathToRscript != null )
-            collection.PATH_TO_RSCRIPT = pathToRscript;
-        if ( anotherSearchPath != null ) {
-            List<String> x = new ArrayList<String>(collection.PATH_TO_RESOURCES);
-            x.add(anotherSearchPath);
-            collection.PATH_TO_RESOURCES = x;
-        }
-        RScriptExecutor executor = new RScriptExecutor(collection, exceptOnError);
-        executor.callRScripts(script);
-    }
 
     @Test
-    public void testPublic() { testOne(publicRScript, null, null, true); }
+    public void testRscriptExists() {
-
+        Assert.assertTrue(RScriptExecutor.RSCRIPT_EXISTS, "Rscript not found in environment ${PATH}");
-    @Test(expectedExceptions = UserException.class)
-    public void testNonExistantScriptException() { testOne("does_not_exist.R", null, null, true); }
-
-    @Test()
-    public void testNonExistantScriptNoException() { testOne("does_not_exist.R", null, null, false); }
-
-    @Test(expectedExceptions = UserException.class)
-    public void testNonExistantRScriptException() { testOne(publicRScript, "badRScriptValue", null, true); }
-
-    @Test()
-    public void testNonExistantRScriptNoException() { testOne(publicRScript, "badRScriptValue", null, false); }
-
-    @Test()
-    public void testScriptInNewPath() throws IOException {
-        File t = createTempFile("myTestScript", ".R");
-        FileUtils.writeStringToFile(t, testrscript);
-        testOne(t.getName(), null, t.getParent(), true);
     }
-}
+
+    @Test(dependsOnMethods = "testRscriptExists")
+    public void testExistingScript() {
+        File script = writeScript(HELLO_WORLD_SCRIPT);
+        try {
+            RScriptExecutor executor = new RScriptExecutor();
+            executor.addScript(script);
+            executor.setExceptOnError(true);
+            Assert.assertTrue(executor.exec(), "Exec failed");
+        } finally {
+            FileUtils.deleteQuietly(script);
+        }
+    }
+
+    @Test(dependsOnMethods = "testRscriptExists", expectedExceptions = RScriptExecutorException.class)
+    public void testNonExistantScriptException() {
+        RScriptExecutor executor = new RScriptExecutor();
+        executor.setExceptOnError(true);
+        executor.addScript(new File("does_not_exists.R"));
+        executor.exec();
+    }
+
+    @Test(dependsOnMethods = "testRscriptExists")
+    public void testNonExistantScriptNoException() {
+        logger.warn("Testing that warning is printed an no exception thrown for missing script.");
+        RScriptExecutor executor = new RScriptExecutor();
+        executor.setExceptOnError(false);
+        executor.addScript(new File("does_not_exists.R"));
+        Assert.assertFalse(executor.exec(), "Exec should have returned false when the job failed");
+    }
+
+    @Test(dependsOnMethods = "testRscriptExists")
+    public void testLibrary() {
+        File script = writeScript(GSALIB_LOADED_SCRIPT);
+        try {
+            RScriptExecutor executor = new RScriptExecutor();
+            executor.addScript(script);
+            executor.addLibrary(RScriptLibrary.GSALIB);
+            executor.setExceptOnError(true);
+            Assert.assertTrue(executor.exec(), "Exec failed");
+        } finally {
+            FileUtils.deleteQuietly(script);
+        }
+    }
+
+    @Test(dependsOnMethods = "testRscriptExists", expectedExceptions = RScriptExecutorException.class)
+    public void testLibraryMissing() {
+        File script = writeScript(GSALIB_LOADED_SCRIPT);
+        try {
+            RScriptExecutor executor = new RScriptExecutor();
+            executor.addScript(script);
+            // GSALIB is not added nor imported in the script
+            executor.setExceptOnError(true);
+            executor.exec();
+        } finally {
+            FileUtils.deleteQuietly(script);
+        }
+    }
+
+    private File writeScript(String content) {
+        return IOUtils.writeTempFile(content, "myTestScript", ".R");
+    }
+}

public/java/test/org/broadinstitute/sting/utils/runtime/ProcessControllerUnitTest.java

@@ -168,7 +168,7 @@ public class ProcessControllerUnitTest extends BaseTest {
         File input = null;
         try {
             String fileText = "Hello from file";
-            input = IOUtils.writeTempFile(fileText, "stdin.", ".txt", null);
+            input = IOUtils.writeTempFile(fileText, "stdin.", ".txt");
 
             ProcessSettings job = new ProcessSettings(new String[] {"cat"});
             job.getStdoutSettings().setBufferSize(-1);

public/java/test/org/broadinstitute/sting/utils/runtime/RuntimeUtilsUnitTest.java

@@ -0,0 +1,41 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.runtime;
+
+import org.broadinstitute.sting.BaseTest;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+public class RuntimeUtilsUnitTest extends BaseTest {
+    @Test
+    public void testWhichExists() {
+        Assert.assertNotNull(RuntimeUtils.which("ls"), "Unable to locate ls");
+    }
+
+    @Test
+    public void testWhichNotExists() {
+        Assert.assertNull(RuntimeUtils.which("does_not_exist"), "Found nonexistent binary: does_not_exist");
+    }
+}

public/packages/AnalyzeCovariates.xml

@@ -7,11 +7,8 @@
       <!-- Recalibration analysis script -->
       <class name="org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates" />
       <package name="org.broadinstitute.sting.gatk.walkers.recalibration" />
+      <!-- Supplemental scripts for graph generation, etc. -->
+      <dir name="org/broadinstitute/sting/analyzecovariates" includes="**/*.R" />
     </dependencies>
   </executable>
-  <resources>
-    <!-- Supplemental scripts for graph generation, etc. -->
-    <file name="public/R/plot_residualError_OtherCovariate.R" />
-    <file name="public/R/plot_residualError_QualityScoreCovariate.R" />
-  </resources>
 </package>

public/packages/GATKEngine.xml

@@ -33,7 +33,9 @@
       <!-- Workaround - depend on the logger impl required by JEXL -->
       <package name="org.apache.commons.logging.impl" />
       <!-- R packages -->
-      <dir name="org/broadinstitute/sting/utils/R" includes="*.tar.gz" />
+      <dir name="org/broadinstitute/sting/utils/R" includes="**/*.tar.gz" />
+      <!-- All R scripts in org.broadinstitute.sting -->
+      <dir name="org/broadinstitute/sting" includes="**/*.R" />
     </dependencies>
   </executable>
   <resources>

public/packages/GenomeAnalysisTK.xml

@@ -19,7 +19,6 @@
     <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java" />
     <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java" />
     <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java" />
-    <file name="public/R/plot_Tranches.R" />
     <file name="public/R/titvFPEst.R" />
   </resources>
   <release>

public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala

@@ -131,7 +131,7 @@ class QCommandLine extends CommandLineProgram with Logging {
 
           val pdfFile = new File(jobStringName + ".pdf")
           logger.info("Plotting JobLogging GATKReport to file " + pdfFile)
-          QJobReport.plotReport(settings.rScriptArgs, reportFile, pdfFile)
+          QJobReport.plotReport(reportFile, pdfFile)
         }
       }
     }

public/scala/src/org/broadinstitute/sting/queue/engine/QGraphSettings.scala

@@ -28,7 +28,6 @@ import java.io.File
 import org.broadinstitute.sting.queue.QSettings
 import org.broadinstitute.sting.queue.util.SystemUtils
 import org.broadinstitute.sting.commandline.{Advanced, ArgumentCollection, Argument}
-import org.broadinstitute.sting.utils.R.RScriptExecutor
 
 /**
  * Command line options for a QGraph.
@@ -77,9 +76,6 @@ class QGraphSettings {
   @Argument(fullName="disableJobReport", shortName="disabpleJobReport", doc="If provided, we will not create a job report", required=false)
   var disableJobReport: Boolean = false
 
-  @ArgumentCollection
-  var rScriptArgs = new RScriptExecutor.RScriptArgumentCollection
-
   @ArgumentCollection
   val qSettings = new QSettings
 }

public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala

@@ -29,7 +29,6 @@ import org.broadinstitute.sting.gatk.report.{GATKReportTable, GATKReport}
 import org.broadinstitute.sting.utils.exceptions.UserException
 import org.broadinstitute.sting.queue.engine.JobRunInfo
 import java.io.{FileOutputStream, PrintStream, File}
-import org.broadinstitute.sting.utils.R.RScriptExecutor.RScriptArgumentCollection
 import org.broadinstitute.sting.utils.R.{RScriptLibrary, RScriptExecutor}
 import org.broadinstitute.sting.utils.io.Resource
 
@@ -104,8 +103,8 @@ object QJobReport {
     stream.close()
   }
 
-  def plotReport(args: RScriptArgumentCollection, reportFile: File, pdfFile: File) {
+  def plotReport(reportFile: File, pdfFile: File) {
-    val executor = new RScriptExecutor(args, false) // don't except on error
+    val executor = new RScriptExecutor
     executor.addLibrary(RScriptLibrary.GSALIB)
     executor.addScript(new Resource(JOB_REPORT_QUEUE_SCRIPT, classOf[QJobReport]))
     executor.addArgs(reportFile.getAbsolutePath, pdfFile.getAbsolutePath)