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Updating Rscript path doc text for Broad users

This commit is contained in:
Ryan Poplin 2011-09-21 15:22:26 -04:00
parent 6592972f82
commit 2585fc3d6c
3 changed files with 3 additions and 3 deletions
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2
public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
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@ -114,7 +114,7 @@ public class AnalyzeCovariates extends CommandLineProgram {
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/";
@Argument(fullName = "path_to_Rscript", shortName = "Rscript", doc = "The path to your implementation of Rscript. For Broad users this is maybe /broad/tools/apps/R-2.6.0/bin/Rscript", required = false)
@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/";

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -155,7 +155,7 @@ 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/tools/apps/R-2.6.0/bin/Rscript", required=false)
@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="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;

2
public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutor.java
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@ -53,7 +53,7 @@ public class RScriptExecutor {
public static class RScriptArgumentCollection {
@Advanced
@Argument(fullName = "path_to_Rscript", shortName = "Rscript", doc = "The path to your implementation of Rscript. For Broad users this is maybe /broad/tools/apps/R-2.6.0/bin/Rscript", required = false)
@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)
public String PATH_TO_RSCRIPT = "Rscript";
@Advanced