Null check to docker volumes

Author: bbimber

primeseq/src/org/labkey/primeseq/PrimeseqModule.java

@@ -72,8 +72,6 @@ protected void init()
     @Override
     protected void doStartupAfterSpringConfig(ModuleContext moduleContext)
     {
-        SequencePipelineService.get().registerResourceSettings(new ExacloudResourceSettings());
-
         SystemMaintenance.addTask(new ClusterMaintenanceTask());
 
         ClusterService.get().registerResourceAllocator(new BlastPipelineJobResourceAllocator.Factory());
@@ -109,6 +107,8 @@ public PipelineStartup()
             }
             else
             {
+                SequencePipelineService.get().registerResourceSettings(new ExacloudResourceSettings());
+
                 SequencePipelineService.get().registerPipelineStep(new BismarkWrapper.Provider());
                 SequencePipelineService.get().registerPipelineStep(new BismarkWrapper.MethylationExtractorProvider());
 

primeseq/src/org/labkey/primeseq/pipeline/ExacloudResourceSettings.java

@@ -83,7 +83,7 @@ private File convertHomeGroups(File input)
         if (input.getPath().startsWith("/home/groups/"))
         {
             String folderName = input.getPath().replaceAll("^/home/groups/", "").split("/")[0];
-            return new File("/home/groups/" + folderName);
+            return new File("/home/groups/", folderName);
         }
 
         return input;
@@ -92,6 +92,7 @@ private File convertHomeGroups(File input)
     @Override
     public @Nullable File inferDockerVolume(File input)
     {
+        input = input.isDirectory() ? input : input.getParentFile();
         if (input.getPath().startsWith("/home/exacloud/gscratch"))
         {
             return new File("/home/exacloud/gscratch");