Remove unused code

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/ReferenceGenomeManager.java

@@ -103,6 +103,11 @@ public void cacheGenomeLocally(ReferenceGenome genome, Logger log) throws Pipeli
         }
 
         File localCacheDir = SequencePipelineService.get().getRemoteGenomeCacheDirectory();
+        if (localCacheDir == null)
+        {
+            throw new PipelineJobException("RemoteGenomeCacheDirectory was not set");
+        }
+
         if (isUpToDate(genome))
         {
             log.debug("Genome up-to-date, will not repeat rsync: " + genome.getGenomeId());

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequencePipelineService.java

@@ -98,11 +98,6 @@ static public void setInstance(SequencePipelineService instance)
      */
     abstract public String getDockerCommand();
 
-    /**
-     * This allows instances to supply a user that will be passed to 'docker login'. This is rarely needed. It can be set using DOCKER_USER in pipelineConfig.xml
-     */
-    abstract public String getDockerUser();
-
     abstract public List<File> getSequenceJobInputFiles(PipelineJob job);
 
     /**

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequencePipelineServiceImpl.java

@@ -457,18 +457,6 @@ public String getDockerCommand()
         return "docker";
     }
 
-    @Override
-    public String getDockerUser()
-    {
-        String val = PipelineJobService.get().getConfigProperties().getSoftwarePackagePath("DOCKER_USER");
-        if (StringUtils.trimToNull(val) != null)
-        {
-            return val;
-        }
-
-        return null;
-    }
-
     @Override
     public List<File> getSequenceJobInputFiles(PipelineJob job)
     {