Use external /tmp directory when running seurat docker jobs

Author: bbimber

singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellPipelineStep.java

@@ -278,9 +278,11 @@ public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerC
             }
 
             writer.println("\t-v \"${WD}:/work\" \\");
+            writer.println("\t-v \"/tmp:/tmp\" \\");
             writer.println("\t-v \"${HOME}:/homeDir\" \\");
             writer.println("\t-u $UID \\");
             writer.println("\t-e USERID=$UID \\");
+            writer.println("\t-e TMPDIR=/tmp \\");
             writer.println("\t-w /work \\");
             //NOTE: this seems to disrupt packages installed into home
             //writer.println("\t-e HOME=/homeDir \\");

singlecell/resources/chunks/MergeSeurat.R

@@ -2,6 +2,7 @@ if (length(seuratObjects) == 1) {
     print('There is only one seurat object, no need to merge')
     newSeuratObjects <- seuratObjects
 } else {
+    doDiet <- exists('doDiet') && doDiet
     if (exists('doDiet') && doDiet) {
         print('Running DietSeurat on inputs')
         for (datasetId in seuratObjects) {
@@ -11,7 +12,7 @@ if (length(seuratObjects) == 1) {
         gc()
     }
 
-    newSeuratObjects[[projectName]] <- CellMembrane::MergeSeuratObjs(seuratObjects, projectName = projectName)
+    newSeuratObjects[[projectName]] <- CellMembrane::MergeSeuratObjs(seuratObjects, projectName = projectName, doGC = doDiet)
 }
 
 # Cleanup