Test fix

Author: bbimber

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

@@ -289,7 +289,7 @@ protected boolean isThrowNonZeroExits()
         return _throwNonZeroExits;
     }
 
-    protected File resolveFileInPath(String exe, @Nullable String packageName, boolean throwIfNotFound)
+    protected static File resolveFileInPath(String exe, @Nullable String packageName, boolean throwIfNotFound)
     {
         File fn;
         String path;

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

@@ -51,19 +51,7 @@ public String getVersion() throws PipelineJobException
 
     public static File getPicardJar()
     {
-        String path = PipelineJobService.get().getConfigProperties().getSoftwarePackagePath("PICARDPATH");
-        if (path != null)
-        {
-            return new File(path);
-        }
-
-        path = PipelineJobService.get().getConfigProperties().getSoftwarePackagePath(SequencePipelineService.SEQUENCE_TOOLS_PARAM);
-        if (path == null)
-        {
-            path = PipelineJobService.get().getAppProperties().getToolsDirectory();
-        }
-
-        return path == null ? null : new File(path, "picard.jar");
+        return resolveFileInPath("picard.jar", "PICARDPATH", true);
     }
 
     protected File getJar()

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java

@@ -60,7 +60,6 @@
 import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
 import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenomeManager;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
-import org.labkey.api.sequenceanalysis.run.CreateSequenceDictionaryWrapper;
 import org.labkey.api.util.FileType;
 import org.labkey.api.util.Job;
 import org.labkey.api.util.JobRunner;