Update ParagraphStep/docker execution

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/DockerWrapper.java

@@ -11,6 +11,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.io.PrintWriter;
+import java.util.Arrays;
 import java.util.List;
 
 public class DockerWrapper extends AbstractCommandWrapper
@@ -29,7 +30,7 @@ public void setTmpDir(File tmpDir)
         _tmpDir = tmpDir;
     }
 
-    public void execute(List<String> containerArgs, File workDir, PipelineOutputTracker tracker) throws PipelineJobException
+    public void executeWithDocker(List<String> containerArgs, File workDir, PipelineOutputTracker tracker) throws PipelineJobException
     {
         File localBashScript = new File(workDir, "docker.sh");
         File dockerBashScript = new File(workDir, "dockerRun.sh");
@@ -77,6 +78,8 @@ public void execute(List<String> containerArgs, File workDir, PipelineOutputTrac
         {
             throw new PipelineJobException(e);
         }
+
+        execute(Arrays.asList("/bin/bash", localBashScript.getPath()));
     }
 
     public File ensureLocalCopy(File input, File workingDirectory, PipelineOutputTracker output) throws PipelineJobException

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java

@@ -189,7 +189,7 @@ else if (header.getReadGroups().size() > 1)
                 paragraphArgs.add("--logfile");
                 paragraphArgs.add(new File("/work/paragraph.log").getPath());
 
-                dockerWrapper.execute(paragraphArgs, ctx.getWorkingDirectory());
+                dockerWrapper.executeWithDocker(paragraphArgs, ctx.getWorkingDirectory(), ctx.getFileManager());
 
                 File genotypes = new File(ctx.getWorkingDirectory(), "genotypes.vcf.gz");
                 if (!genotypes.exists())