Support -num_threads for BLASTn

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/TagPcrSummaryStep.java

@@ -81,7 +81,7 @@ public void init(SequenceAnalysisJobSupport support) throws PipelineJobException
 
         for (ReferenceGenome rg : support.getCachedGenomes()) {
             SimpleFilter filter = new SimpleFilter(FieldKey.fromString("libraryid"), rg.getGenomeId());
-            filter.addCondition(FieldKey.fromString("datedisabled"), CompareType.ISBLANK);
+            filter.addCondition(FieldKey.fromString("datedisabled"), null, CompareType.ISBLANK);
 
             TableSelector ts = new TableSelector(ti, PageFlowUtil.set("objectid", "container"), filter, null);
             if (ts.exists())
@@ -255,6 +255,13 @@ public void execute(File bamFile, File referenceFasta, File outputTable, File pr
             args.add("--blast-db-path");
             args.add(blastDbBase.getPath());
 
+            Integer maxThreads = SequencePipelineService.get().getMaxThreads(getLogger());
+            if (maxThreads != null)
+            {
+                args.add("--blast-threads");
+                args.add(maxThreads.toString());
+            }
+
             execute(args);
         }
     }

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/BlastNWrapper.java

@@ -3,6 +3,7 @@
 import org.apache.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.pipeline.PipelineJobException;
+import org.labkey.api.pipeline.PipelineJobService;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper;
 
@@ -70,6 +71,17 @@ public void doRemoteBlast(File fasta, File output, @Nullable List<String> extraP
         args.add("-query");
         args.add(fasta.getPath());
         args.add("-remote");
+
+        if (PipelineJobService.get().getLocationType() != PipelineJobService.LocationType.WebServer)
+        {
+            Integer maxThreads = SequencePipelineService.get().getMaxThreads(getLogger());
+            if (maxThreads != null)
+            {
+                args.add("-num_threads");
+                args.add(maxThreads.toString());
+            }
+        }
+
         args.add("-out");
         args.add(output.getPath());
 

blast/src/org/labkey/blast/BLASTWrapper.java

@@ -68,6 +68,16 @@ public File runBlastN(String blastDbGuid, File input, File outputFile, Map<Strin
         args.add("-index_name");
         args.add(db.getPath());
 
+        if (PipelineJobService.get().getLocationType() != PipelineJobService.LocationType.WebServer)
+        {
+            Integer maxThreads = SequencePipelineService.get().getMaxThreads(getLogger());
+            if (maxThreads != null)
+            {
+                args.add("-num_threads");
+                args.add(maxThreads.toString());
+            }
+        }
+
         args.add("-out");
         args.add(outputFile.getPath());