From 2585fc3d6cc4dd873eed2868fef8335d7e40a504 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Wed, 21 Sep 2011 15:22:26 -0400
Subject: [PATCH] Updating Rscript path doc text for Broad users

---
 .../sting/analyzecovariates/AnalyzeCovariates.java              | 2 +-
 .../gatk/walkers/variantrecalibration/VariantRecalibrator.java  | 2 +-
 .../src/org/broadinstitute/sting/utils/R/RScriptExecutor.java   | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
index 7ea515591..1ef452a5c 100755
--- a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
+++ b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
@@ -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/";
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 529d17285..89e702b64 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -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;
diff --git a/public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutor.java b/public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutor.java
index c0493fe22..58f7942fe 100644
--- a/public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutor.java
+++ b/public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutor.java
@@ -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