Remove debugging code

Author: bbimber

SequenceAnalysis/resources/web/SequenceAnalysis/panel/AlignmentAnalysisPanel.js

@@ -80,7 +80,10 @@ Ext4.define('SequenceAnalysis.panel.AlignmentAnalysisPanel', {
 
                     this.libraryIds = Ext4.unique(libraryIds);
 
-                    this.down('#alignmentCount').update('Alignments to be analyzed: ' + store.getCount());
+                    var target = this.down('#alignmentCount');
+                    if (target) {
+                        target.update('Alignments to be analyzed: ' + store.getCount());
+                    }
                 }
             }
         });

singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellPipelineStep.java

@@ -249,7 +249,6 @@ public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerC
         }
 
         File localBashScript = new File(ctx.getOutputDir(), "dockerWrapper.sh");
-        File rWrapperScript = new File(ctx.getOutputDir(), "rWrapper.sh");
         try (PrintWriter writer = PrintWriters.getPrintWriter(localBashScript))
         {
             writer.println("#!/bin/bash");
@@ -283,7 +282,7 @@ public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerC
             writer.println("\t-w /work \\");
             writer.println("\t-e HOME=/homeDir \\");
             writer.println("\t" + dockerContainerName + " \\");
-            writer.println("\t/bin/bash " + rWrapperScript.getName());
+            writer.println("\tRscript --vanilla " + localRScript.getName());
             writer.println("");
             writer.println("echo 'Bash script complete'");
 
@@ -293,30 +292,11 @@ public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerC
             throw new PipelineJobException(e);
         }
 
-        try (PrintWriter writer = PrintWriters.getPrintWriter(rWrapperScript))
-        {
-            writer.println("#!/bin/bash");
-            writer.println("set -x");
-
-            writer.println("if Rscript --vanilla " + localRScript.getName());
-            writer.println("then");
-            writer.println("\texit 0");
-            writer.println("else");
-            writer.println("\techo \"Rscript exited with value $?\"");
-            writer.println("\texit 0");
-            writer.println("fi");
-        }
-        catch (IOException e)
-        {
-            throw new PipelineJobException(e);
-        }
-
         SimpleScriptWrapper rWrapper = new SimpleScriptWrapper(ctx.getLogger());
         rWrapper.setWorkingDir(ctx.getOutputDir());
         rWrapper.execute(Arrays.asList("/bin/bash", localBashScript.getName()));
 
         localRScript.delete();
-        rWrapperScript.delete();
         localBashScript.delete();
     }
 

singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java

@@ -1249,11 +1249,9 @@ private File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, S
         }
 
         File localBashScript = new File(outputDir, "generateCallsDockerWrapper.sh");
-        File rWrapperScript = new File(outputDir, "generateCallsRWrapper.sh");
         try (PrintWriter writer = PrintWriters.getPrintWriter(localBashScript))
         {
             writer.println("#!/bin/bash");
-            writer.println("set -e");
             writer.println("set -x");
             writer.println("WD=`pwd`");
             writer.println("HOME=`echo ~/`");
@@ -1279,25 +1277,7 @@ private File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, S
             writer.println("\t-w /work \\");
             writer.println("\t-e HOME=/homeDir \\");
             writer.println("\tghcr.io/bimberlab/cellhashr:latest \\");
-            writer.println("\t/bin/bash " + rWrapperScript.getName());
-        }
-        catch (IOException e)
-        {
-            throw new PipelineJobException(e);
-        }
-
-        try (PrintWriter writer = PrintWriters.getPrintWriter(rWrapperScript))
-        {
-            writer.println("#!/bin/bash");
-            writer.println("set -x");
-
-            writer.println("if Rscript --vanilla " + localRScript.getName());
-            writer.println("then");
-            writer.println("\texit 0");
-            writer.println("else");
-            writer.println("\techo \"Rscript exited with value $?\"");
-            writer.println("\texit 0");
-            writer.println("fi");
+            writer.println("\tRscript --vanilla " + localRScript.getName());
         }
         catch (IOException e)
         {
@@ -1335,7 +1315,6 @@ private File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, S
         }
 
         localBashScript.delete();
-        rWrapperScript.delete();
         localRScript.delete();
 
         try