More error reporting

Author: bbimber

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

@@ -283,7 +283,7 @@ 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" + rWrapperScript.getName());
+            writer.println("\t/bin/bash " + rWrapperScript.getName());
             writer.println("");
             writer.println("echo 'Bash script complete'");
 
@@ -316,6 +316,7 @@ public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerC
         rWrapper.execute(Arrays.asList("/bin/bash", localBashScript.getName()));
 
         localRScript.delete();
+        rWrapperScript.delete();
         localBashScript.delete();
     }
 

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

@@ -1234,7 +1234,7 @@ private File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, S
                 Set<String> allowableBarcodes = parameters.getAllowableBarcodeNames();
                 String allowableBarcodeParam = allowableBarcodes != null ? "c('" + StringUtils.join(allowableBarcodes, "','") + "')" : "NULL";
 
-                writer.println("cellhashR::CallAndGenerateReport(rawCountData = '/work/" + citeSeqCountOutDir.getName() + "', reportFile = '/work/" + htmlFile.getName() + "', callFile = '/work/" + callsFile.getName() + "', metricsFile = '/work/" + metricsFile.getName() + "', cellbarcodeWhitelist  = " + cellbarcodeWhitelist + ", barcodeWhitelist = " + allowableBarcodeParam + ", title = '" + parameters.getReportTitle() + "', methods = c('" + StringUtils.join(methodNames, "','") + "'))");
+                writer.println("f <- cellhashR::CallAndGenerateReport(rawCountData = '/work/" + citeSeqCountOutDir.getName() + "', reportFile = '/work/" + htmlFile.getName() + "', callFile = '/work/" + callsFile.getName() + "', metricsFile = '/work/" + metricsFile.getName() + "', cellbarcodeWhitelist  = " + cellbarcodeWhitelist + ", barcodeWhitelist = " + allowableBarcodeParam + ", title = '" + parameters.getReportTitle() + "', methods = c('" + StringUtils.join(methodNames, "','") + "'))");
                 writer.println("print('Rmarkdown complete')");
 
             }
@@ -1248,7 +1248,8 @@ private File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, S
             log.info("script exists, re-using: " + localRScript.getPath());
         }
 
-        File localBashScript = new File(outputDir, "generateCallsWrapper.sh");
+        File localBashScript = new File(outputDir, "generateCallsDockerWrapper.sh");
+        File rWrapperScript = new File(outputDir, "generateCallsRWrapper.sh");
         try (PrintWriter writer = PrintWriters.getPrintWriter(localBashScript))
         {
             writer.println("#!/bin/bash");
@@ -1278,7 +1279,25 @@ 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("\tRscript --vanilla " + localRScript.getName());
+            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");
         }
         catch (IOException e)
         {
@@ -1315,6 +1334,10 @@ private File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, S
             throw new PipelineJobException("Unable to find HTO calls file: " + callsFile.getPath());
         }
 
+        localBashScript.delete();
+        rWrapperScript.delete();
+        localRScript.delete();
+
         try
         {
             for (File f : toDelete)