Ensure we use the cached genome resources

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AlignerIndexUtil.java

@@ -48,9 +48,14 @@ public static boolean copyIndexIfExists(PipelineContext ctx, AlignmentOutputImpl
         return verifyOrCreateCachedIndex(ctx, ctx.getWorkDir(), output, localName, webserverName, genome, forceCopyLocal);
     }
 
-    public static File getWebserverIndexDir(ReferenceGenome genome, String name)
+    public static File getIndexDir(ReferenceGenome genome, String name)
     {
-        return new File(genome.getSourceFastaFile().getParentFile(), (genome.isTemporaryGenome() ? "" : INDEX_DIR + "/") + name);
+        return getIndexDir(genome, name, false);
+    }
+
+    public static File getIndexDir(ReferenceGenome genome, String name, boolean useWebserverDir)
+    {
+        return new File(useWebserverDir ? genome.getSourceFastaFile().getParentFile() : genome.getWorkingFastaFile().getParentFile(), (genome.isTemporaryGenome() ? "" : INDEX_DIR + "/") + name);
     }
 
     /**
@@ -62,7 +67,7 @@ private static boolean verifyOrCreateCachedIndex(PipelineContext ctx, @Nullable
         if (genome != null)
         {
             //NOTE: when we cache the indexes with the source FASTA genome, we store all aligners under the folder /alignerIndexes.  When these are temporary genomes, they're top-level
-            File webserverIndexDir = getWebserverIndexDir(genome, webserverName);
+            File webserverIndexDir = getIndexDir(genome, webserverName, true);
             if (webserverIndexDir.exists())
             {
                 ctx.getLogger().info("previously created index found, no need to recreate");

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/CellRangerWrapper.java

@@ -336,7 +336,7 @@ public AlignmentOutput performAlignment(Readset rs, File inputFastq1, @Nullable
             File gtfFile = getPipelineCtx().getSequenceSupport().getCachedData(gtfId);
             output.addInput(gtfFile, GTF_FILE);
 
-            File indexDir = AlignerIndexUtil.getWebserverIndexDir(referenceGenome, getIndexCachedDirName(getPipelineCtx().getJob()));
+            File indexDir = AlignerIndexUtil.getIndexDir(referenceGenome, getIndexCachedDirName(getPipelineCtx().getJob()));
             args.add("--transcriptome=" + indexDir.getPath());
 
             getWrapper().setWorkingDir(outputDirectory);

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SNPEffStep.java

@@ -65,7 +65,7 @@ public static File checkOrCreateIndex(SequenceAnalysisJobSupport support, Logger
     {
         log.debug("checking for index");
 
-        File snpEffBaseDir = AlignerIndexUtil.getWebserverIndexDir(genome, NAME);
+        File snpEffBaseDir = AlignerIndexUtil.getIndexDir(genome, NAME);
         File geneFile = support.getCachedData(geneFileId);
         if (geneFile == null || !geneFile.exists())
         {