Bugfix to DeepVariant docker command

BimberLab · Jan 22, 2024 · 207b83e · 207b83e
1 parent a62258d
commit 207b83e
Showing 1 changed file with 1 addition 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
@@ -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());