Preferentially use remote cached genome

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java

@@ -383,7 +383,7 @@ private File runGenotypeGVCFs(PipelineJob job, JobContext ctx, ProcessVariantsHa
                 toolParams.add("--genomicsdb-shared-posixfs-optimizations");
             }
 
-            wrapper.execute(genome.getSourceFastaFile(), outputVcf, toolParams, inputVcf);
+            wrapper.execute(genome.getWorkingFastaFile(), outputVcf, toolParams, inputVcf);
 
             action.addOutput(outputVcf, "VCF", outputVcf.exists(), true);
             action.setEndTime(new Date());

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

@@ -56,6 +56,20 @@ public boolean isTemporaryGenome() {
     @Override
     public @NotNull File getWorkingFastaFile()
     {
+        if (SequencePipelineService.get().isRemoteGenomeCacheUsed())
+        {
+            File ret = SequencePipelineService.get().getRemoteGenomeCacheDirectory();
+            if (ret != null)
+            {
+                ret = new File(ret, getGenomeId().toString());
+                ret = new File(ret, _sourceFasta.getName());
+                if (ret.exists())
+                {
+                    return ret;
+                }
+            }
+        }
+
         return _workingFasta == null ? _sourceFasta : _workingFasta;
     }
 

blast/src/org/labkey/blast/pipeline/BlastDatabasePipelineJob.java

@@ -55,7 +55,7 @@ public BlastDatabasePipelineJob(Container c, User user, ActionURL url, PipeRoot
         setLogFile(new File(BLASTManager.get().getDatabaseDir(c, true), "blast-" + _databaseGuid + ".log"));
 
         ReferenceGenome rg = SequenceAnalysisService.get().getReferenceGenome(_libraryId, user);
-        _fasta = rg.getSourceFastaFile();
+        _fasta = rg.getWorkingFastaFile();
         _databaseDir = BLASTManager.get().getDatabaseDir(getContainer(), true);
         possiblyCreateDbRecord();
     }