Remove direct access to GenomicsDBImport

Author: bbimber

SequenceAnalysis/pipeline_code/sequence_tools_install.sh

@@ -309,10 +309,6 @@ then
     unzip gatk-4.6.1.0.zip
 
     cp ./gatk-4.6.1.0/gatk-package-4.6.1.0-local.jar $LKTOOLS_DIR/GenomeAnalysisTK4.jar
-
-    wget $WGET_OPTS https://github.com/GenomicsDB/GenomicsDB/releases/download/v1.4.3/consolidate_genomicsdb_array
-    chmod +x consolidate_genomicsdb_array
-    cp consolidate_genomicsdb_array $LKTOOLS_DIR/consolidate_genomicsdb_array
 else
     echo "Already installed"
 fi

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java

@@ -158,8 +158,6 @@
 import org.labkey.sequenceanalysis.run.reference.VirusReferenceLibraryStep;
 import org.labkey.sequenceanalysis.run.util.CombineGVCFsHandler;
 import org.labkey.sequenceanalysis.run.util.FastqcRunner;
-import org.labkey.sequenceanalysis.run.util.GenomicsDBAppendHandler;
-import org.labkey.sequenceanalysis.run.util.GenomicsDBImportHandler;
 import org.labkey.sequenceanalysis.run.util.SVAnnotateStep;
 import org.labkey.sequenceanalysis.run.variant.DepthOfCoverageHandler;
 import org.labkey.sequenceanalysis.run.variant.GenotypeConcordanceStep;
@@ -397,8 +395,6 @@ public static void registerPipelineSteps()
         SequenceAnalysisService.get().registerFileHandler(new RecalculateSequenceMetricsHandler());
         SequenceAnalysisService.get().registerFileHandler(new ListVcfSamplesHandler());
         SequenceAnalysisService.get().registerFileHandler(new MultiQCBamHandler());
-        SequenceAnalysisService.get().registerFileHandler(new GenomicsDBImportHandler());
-        SequenceAnalysisService.get().registerFileHandler(new GenomicsDBAppendHandler());
         SequenceAnalysisService.get().registerFileHandler(new MergeLoFreqVcfHandler());
         SequenceAnalysisService.get().registerFileHandler(new PangolinHandler());
         SequenceAnalysisService.get().registerFileHandler(new NextCladeHandler());

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

@@ -644,7 +644,7 @@ else if (genomeIds.isEmpty())
 
                     wrapper.execute(genome, vcfsToProcess, workingDestinationWorkspaceFolder, intervals, options, _append);
 
-                    if (ctx.getParams().optBoolean("consolidate", true))
+                    if (ctx.getParams().optBoolean("consolidate", false))
                     {
                         ctx.getLogger().info("Will consolidate the workspace using consolidate_genomicsdb_array");
                         doConsolidate(ctx, workingDestinationWorkspaceFolder, genome);