Dont set tmpdir for DeepVariant/docker

BimberLab · Jan 22, 2024 · 97ace2f · 97ace2f
1 parent c522d20
commit 97ace2f
Showing 1 changed file with 0 additions and 1 deletion.
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java
@@ -248,7 +248,6 @@ public void execute(File inputBam, File refFasta, File outputGvcf, PipelineOutpu
                 writer.println("\t-v \"${WD}:/work\" \\");
                 writer.println("\t-v \"${HOME}:/homeDir\" \\");
                 writer.println("\t-u $UID \\");
-                writer.println("\t-e TMPDIR=/work/tmpDir \\");
                 writer.println("\t-e USERID=$UID \\");
                 writer.println("\t--entrypoint /bin/bash \\");
                 writer.println("\t-w /work \\");