Bugfix to DeepVariant docker command

bbimber · bbimber · commit a62258df0423 · 2024-01-20T11:15:30.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java
@@ -265,7 +265,7 @@ public void execute(File inputBam, File refFasta, File outputGvcf, PipelineOutpu
                 throw new PipelineJobException(e);
             }
 
-            execute(Arrays.asList("/bin/bash/", localBashScript.getPath()));
+            execute(Arrays.asList("/bin/bash", localBashScript.getPath()));
 
             if (!outputGvcf.exists())
             {

Original file line number	Diff line number	Diff line change
`@@ -265,7 +265,7 @@ public void execute(File inputBam, File refFasta, File outputGvcf, PipelineOutpu`
`265`	`265`	`throw new PipelineJobException(e);`
`266`	`266`	`}`
`267`	`267`
`268`		`- execute(Arrays.asList("/bin/bash/", localBashScript.getPath()));`
	`268`	`+ execute(Arrays.asList("/bin/bash", localBashScript.getPath()));`
`269`	`269`
`270`	`270`	`if (!outputGvcf.exists())`
`271`	`271`	`{`