From 207b83eee9502f15a34452687d4e84082c54e498 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Sun, 21 Jan 2024 16:19:11 -0800
Subject: [PATCH] Bugfix to DeepVariant docker command

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

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java
index cfae02936..148c65013 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java
@@ -246,6 +246,7 @@ public void execute(File inputBam, File refFasta, File outputGvcf, PipelineOutpu
                 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 \\");
                 writer.println("\tgoogle/deepvariant:" + binVersion + " \\");
                 writer.println("\t/work/" + dockerBashScript.getName());