Update FastqcRunner JAR path

bbimber · web-flow · commit 147c3ce7e167 · 2023-09-01T06:15:38.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java
@@ -373,7 +373,7 @@ private List<String> getBaseParams() throws FileNotFoundException
             throw new RuntimeException("Not found: " + jbzip2.getPath());
         }
 
-        File htsjdkJar = new File(libDir, "htsjdk-3.0.1.jar");
+        File htsjdkJar = new File(libDir, "htsjdk-4.0.0.jar");
         if (!htsjdkJar.exists())
         {
             throw new RuntimeException("Not found: " + htsjdkJar.getPath());

Original file line number	Diff line number	Diff line change
`@@ -373,7 +373,7 @@ private List<String> getBaseParams() throws FileNotFoundException`
`373`	`373`	`throw new RuntimeException("Not found: " + jbzip2.getPath());`
`374`	`374`	`}`
`375`	`375`
`376`		`- File htsjdkJar = new File(libDir, "htsjdk-3.0.1.jar");`
	`376`	`+ File htsjdkJar = new File(libDir, "htsjdk-4.0.0.jar");`
`377`	`377`	`if (!htsjdkJar.exists())`
`378`	`378`	`{`
`379`	`379`	`throw new RuntimeException("Not found: " + htsjdkJar.getPath());`