Allow GenotypeGVCFs to disable file locking for TileDB

Author: bbimber

SequenceAnalysis/resources/web/SequenceAnalysis/panel/VariantProcessingPanel.js

@@ -236,6 +236,12 @@ Ext4.define('SequenceAnalysis.panel.VariantProcessingPanel', {
 				label: 'Allow Old RMS Mapping Data',
 				description: 'This must be checked to allow processing of gVCFs generated by GATK3.',
 				defaultValue: false
+			},{
+				fieldXtype: 'checkbox',
+				name: 'disableFileLocking',
+				label: 'Disable File Locking',
+				description: 'This applies to GenomicsDB inputs only. Certain filesystems do not support file locking, including NFS and Lustre.  If your data will be processed on a filesystem that does not support locking, check this.',
+				defaultValue: true
 			},{
 				fieldXtype: 'checkbox',
 				name: 'doCopyInputs',

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

@@ -367,6 +367,12 @@ private File runGenotypeGVCFs(PipelineJob job, JobContext ctx, ProcessVariantsHa
                 });
             }
 
+            if (ctx.getParams().optBoolean("disableFileLocking", false))
+            {
+                ctx.getLogger().debug("Disabling file locking for TileDB");
+                wrapper.addToEnvironment("TILEDB_DISABLE_FILE_LOCKING", "1");
+            }
+
             wrapper.execute(genome.getSourceFastaFile(), outputVcf, toolParams, inputVcf);
 
             action.addOutput(outputVcf, "VCF", outputVcf.exists(), true);