Bugfix to nimble version reporting

bbimber · bbimber · commit 7b689ead551d · 2024-11-12T06:29:06.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
@@ -737,9 +737,7 @@ public Integer getNumMismatches()
     private String getVersion(PipelineStepOutput output) throws PipelineJobException
     {
         List<String> nimbleArgs = new ArrayList<>();
-        nimbleArgs.add("/bin/bash");
-        nimbleArgs.add("-c");
-        nimbleArgs.add("python3 -m nimble -v > /work/nimbleVersion.txt");
+        nimbleArgs.add("/bin/bash -c 'python3 -m nimble -v' > /work/nimbleVersion.txt");
 
         runUsingDocker(nimbleArgs, output, null);
 

Original file line number	Diff line number	Diff line change
`@@ -737,9 +737,7 @@ public Integer getNumMismatches()`
`737`	`737`	`private String getVersion(PipelineStepOutput output) throws PipelineJobException`
`738`	`738`	`{`
`739`	`739`	`List<String> nimbleArgs = new ArrayList<>();`
`740`		`- nimbleArgs.add("/bin/bash");`
`741`		`- nimbleArgs.add("-c");`
`742`		`- nimbleArgs.add("python3 -m nimble -v > /work/nimbleVersion.txt");`
	`740`	`+ nimbleArgs.add("/bin/bash -c 'python3 -m nimble -v' > /work/nimbleVersion.txt");`
`743`	`741`
`744`	`742`	`runUsingDocker(nimbleArgs, output, null);`
`745`	`743`