Add external TMPDIR to deepvariant docker command

BimberLab · Jan 23, 2024 · 300300a · 300300a
1 parent fd99e2a
commit 300300a
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java
@@ -247,6 +247,10 @@ public void execute(File inputBam, File refFasta, File outputGvcf, PipelineOutpu
                 writer.println("sudo $DOCKER run --rm=true \\");
                 writer.println("\t-v \"${WD}:/work\" \\");
                 writer.println("\t-v \"${HOME}:/homeDir\" \\");
+                if (!StringUtils.isEmpty(System.getenv("TMPDIR")))
+                {
+                    writer.println("\t-v \"${TMPDIR}:/tmp\" \\");
+                }
                 writer.println("\t-u $UID \\");
                 writer.println("\t-e USERID=$UID \\");
                 writer.println("\t--entrypoint /bin/bash \\");