Debug cellranger/symlinks

bbimber · bbimber · commit 89f4d547af2a · 2025-11-28T07:43:37.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java b/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java
@@ -646,10 +646,7 @@ public File getInclusionListFile(Logger logger) throws PipelineJobException
                 {
                     Path exePath = Files.readSymbolicLink(exe.toPath());
                     logger.debug("cellranger symlink target: " + exePath.toString());
-                    logger.debug("cellranger symlink absolute path: " + exePath.toAbsolutePath());
-                    logger.debug("cellranger symlink realpath path: " + exePath.toRealPath());
-
-                    exe = exePath.toFile();
+                    exe = FileUtil.resolveFile(exePath.toFile());
                     logger.debug("cellranger resolved symlink target: " + exe.getPath());
                 }
                 catch (IOException e)

Original file line number	Diff line number	Diff line change
`@@ -646,10 +646,7 @@ public File getInclusionListFile(Logger logger) throws PipelineJobException`
`646`	`646`	`{`
`647`	`647`	`Path exePath = Files.readSymbolicLink(exe.toPath());`
`648`	`648`	`logger.debug("cellranger symlink target: " + exePath.toString());`
`649`		`- logger.debug("cellranger symlink absolute path: " + exePath.toAbsolutePath());`
`650`		`- logger.debug("cellranger symlink realpath path: " + exePath.toRealPath());`
`651`		`-`
`652`		`- exe = exePath.toFile();`
	`649`	`+ exe = FileUtil.resolveFile(exePath.toFile());`
`653`	`650`	`logger.debug("cellranger resolved symlink target: " + exe.getPath());`
`654`	`651`	`}`
`655`	`652`	`catch (IOException e)`