Use absolute location of cellrange executable

bbimber · bbimber · commit 7de9d4731d10 · 2025-11-26T11:09:21.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java b/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java
@@ -650,7 +650,7 @@ public File getInclusionListFile(Logger logger) throws PipelineJobException
                 }
             }
 
-            File il = new File(exe.getParentFile(), "lib/python/cellranger/barcodes/" + _inclusionListFile);
+            File il = new File(exe.getAbsoluteFile().getParentFile(), "lib/python/cellranger/barcodes/" + _inclusionListFile);
             if (!il.exists())
             {
                 throw new PipelineJobException("Unable to find file: " + il.getPath());

Original file line number	Diff line number	Diff line change
`@@ -650,7 +650,7 @@ public File getInclusionListFile(Logger logger) throws PipelineJobException`
`650`	`650`	`}`
`651`	`651`	`}`
`652`	`652`
`653`		`- File il = new File(exe.getParentFile(), "lib/python/cellranger/barcodes/" + _inclusionListFile);`
	`653`	`+ File il = new File(exe.getAbsoluteFile().getParentFile(), "lib/python/cellranger/barcodes/" + _inclusionListFile);`
`654`	`654`	`if (!il.exists())`
`655`	`655`	`{`
`656`	`656`	`throw new PipelineJobException("Unable to find file: " + il.getPath());`