Debug cellranger/symlink

bbimber · bbimber · commit 845757b954d9 · 2025-11-26T15:21:42.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java b/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java
@@ -643,7 +643,7 @@ public File getInclusionListFile(Logger logger) throws PipelineJobException
             {
                 try
                 {
-                    exe = Files.readSymbolicLink(exe.toPath()).toRealPath().toFile();
+                    exe = Files.readSymbolicLink(exe.toPath()).resolve(exe.getParentFile().toPath()).toFile();
                     logger.debug("cellranger symlink target: " + exe.getPath());
                 }
                 catch (IOException e)

Original file line number	Diff line number	Diff line change
`@@ -643,7 +643,7 @@ public File getInclusionListFile(Logger logger) throws PipelineJobException`
`643`	`643`	`{`
`644`	`644`	`try`
`645`	`645`	`{`
`646`		`- exe = Files.readSymbolicLink(exe.toPath()).toRealPath().toFile();`
	`646`	`+ exe = Files.readSymbolicLink(exe.toPath()).resolve(exe.getParentFile().toPath()).toFile();`
`647`	`647`	`logger.debug("cellranger symlink target: " + exe.getPath());`
`648`	`648`	`}`
`649`	`649`	`catch (IOException e)`