Bugfix to symlink

bbimber · bbimber · commit af83b5211436 · 2025-11-28T12:44:21.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java b/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java
@@ -648,7 +648,13 @@ public File getInclusionListFile(Logger logger) throws PipelineJobException
                     logger.debug("cellranger symlink target: " + exePath);
                     if (!exePath.isAbsolute())
                     {
-                        exePath = exe.getParentFile().toPath().resolve(exePath);
+                        File parent = exe.getParentFile();
+                        if (parent.getPath().endsWith("bin"))
+                        {
+                            parent = parent.getParentFile();
+                        }
+
+                        exePath = parent.toPath().resolve(exePath);
                         logger.debug("resolved symlink target: " + exePath);
                     }
 

Original file line number	Diff line number	Diff line change
`@@ -648,7 +648,13 @@ public File getInclusionListFile(Logger logger) throws PipelineJobException`
`648`	`648`	`logger.debug("cellranger symlink target: " + exePath);`
`649`	`649`	`if (!exePath.isAbsolute())`
`650`	`650`	`{`
`651`		`- exePath = exe.getParentFile().toPath().resolve(exePath);`
	`651`	`+ File parent = exe.getParentFile();`
	`652`	`+ if (parent.getPath().endsWith("bin"))`
	`653`	`+ {`
	`654`	`+ parent = parent.getParentFile();`
	`655`	`+ }`
	`656`	`+`
	`657`	`+ exePath = parent.toPath().resolve(exePath);`
`652`	`658`	`logger.debug("resolved symlink target: " + exePath);`
`653`	`659`	`}`
`654`	`660`