Pass tmpDir to nimble using environment

bbimber · bbimber · commit 9a4feeb7af53 · 2024-12-01T18:22:14.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
@@ -567,7 +567,8 @@ private static boolean runUsingDocker(List<String> nimbleArgs, PipelineStepOutpu
             }
         }
         output.addIntermediateFile(tmpDir);
-        wrapper.setTmpDir(tmpDir);
+        wrapper.setTmpDir(null);
+        wrapper.addToEnvironment("TMPDIR", tmpDir.getPath());
 
         wrapper.addToEnvironment("RUST_BACKTRACE", "1");
 

Original file line number	Diff line number	Diff line change
`@@ -567,7 +567,8 @@ private static boolean runUsingDocker(List<String> nimbleArgs, PipelineStepOutpu`
`567`	`567`	`}`
`568`	`568`	`}`
`569`	`569`	`output.addIntermediateFile(tmpDir);`
`570`		`- wrapper.setTmpDir(tmpDir);`
	`570`	`+ wrapper.setTmpDir(null);`
	`571`	`+ wrapper.addToEnvironment("TMPDIR", tmpDir.getPath());`
`571`	`572`
`572`	`573`	`wrapper.addToEnvironment("RUST_BACKTRACE", "1");`
`573`	`574`