Need force=True in pysam.tabix_index because the index file path exis…

…ts in the object store
galaxyproject · Dec 8, 2017 · 07158e0 · 07158e0
1 parent 2a6e00d
commit 07158e0
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
@@ -763,7 +763,7 @@ def set_meta(self, dataset, **kwd):
             index_file = dataset.metadata.spec['tabix_index'].param.new_file(dataset=dataset)
 
         try:
-            pysam.tabix_index(dataset.file_name, index=index_file.file_name, preset='vcf')
+            pysam.tabix_index(dataset.file_name, index=index_file.file_name, preset='vcf', force=True)
         except Exception as e:
             raise Exception('Error setting VCF.gz metadata: %s' % (str(e)))
         dataset.metadata.tabix_index = index_file