Support GenomicsDB POSIX optimizations flag

Author: bbimber

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

@@ -563,6 +563,11 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
             GenomicsDbImportWrapper wrapper = new GenomicsDbImportWrapper(ctx.getLogger());
             List<String> options = new ArrayList<>(getClientCommandArgs(ctx.getParams()));
 
+            if (ctx.getParams().optBoolean("sharedPosixOptimizations", false))
+            {
+                options.add("--genomicsdb-shared-posixfs-optimizations");
+            }
+
             if (ctx.getParams().optBoolean("disableFileLocking", false))
             {
                 ctx.getLogger().debug("Disabling file locking for TileDB");

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

@@ -32,6 +32,9 @@ public GenomicsDBAppendHandler()
                 ToolParameterDescriptor.create("disableFileLocking", "Disable File Locking", "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.", "checkbox", new JSONObject(){{
                     put("checked", true);
                 }}, true),
+                ToolParameterDescriptor.create("sharedPosixOptimizations", "Use Shared Posix Optimizations", "This enabled optimizations for large shared filesystems, such as lustre.", "checkbox", new JSONObject(){{
+                    put("checked", true);
+                }}, true),
                 ToolParameterDescriptor.create("scatterGather", "Scatter/Gather Options", "If selected, this job will be divided to run job per chromosome.  The final step will take the VCF from each intermediate step and combined to make a final VCF file.", "sequenceanalysis-variantscattergatherpanel", new JSONObject(){{
                     put("defaultValue", "chunked");
                 }}, false)

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

@@ -27,6 +27,9 @@ public GenomicsDBImportHandler()
                 ToolParameterDescriptor.create("disableFileLocking", "Disable File Locking", "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.", "checkbox", new JSONObject(){{
                     put("checked", true);
                 }}, true),
+                ToolParameterDescriptor.create("sharedPosixOptimizations", "Use Shared Posix Optimizations", "This enabled optimizations for large shared filesystems, such as lustre.", "checkbox", new JSONObject(){{
+                    put("checked", true);
+                }}, true),
                 ToolParameterDescriptor.create("scatterGather", "Scatter/Gather Options", "If selected, this job will be divided to run job per chromosome.  The final step will take the VCF from each intermediate step and combined to make a final VCF file.", "sequenceanalysis-variantscattergatherpanel", new JSONObject(){{
                     put("defaultValue", "chunked");
                 }}, false)