From 97ace2f99c06050636e1a51bc14c03ffafb34499 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Sun, 21 Jan 2024 21:27:01 -0800
Subject: [PATCH] Dont set tmpdir for DeepVariant/docker

---
 .../sequenceanalysis/run/analysis/DeepVariantAnalysis.java       | 1 -
 1 file changed, 1 deletion(-)

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java
index 7ce9fc422..dcd4005af 100644
--- 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 \\");