diff --git a/lib/galaxy/jobs/runners/pbs.py b/lib/galaxy/jobs/runners/pbs.py
index 50cf382177c..384933cdd96 100644
--- a/lib/galaxy/jobs/runners/pbs.py
+++ b/lib/galaxy/jobs/runners/pbs.py
@@ -112,16 +112,17 @@ class PBSJobRunner( object ):
                 if os.access(input_fname, os.R_OK):
                     if stagein != '':
                         stagein += ','
-                    stagein += "%s/%s@%s:%s/%s" % (self.app.config.pbs_instance_path, input_fname, self.app.config.pbs_dataset_server, self.app.config.pbs_dataset_path, input_fname)
+                    # pathnames are now absolute
+                    stagein += "%s@%s:%s" % (input_fname, self.app.config.pbs_dataset_server, input_fname)
             for output_fname in job_wrapper.get_output_fnames():
                 if os.access(output_fname, os.R_OK):
                     if stageout != '':
                         stageout += ','
-                    stageout += "%s/%s@%s:%s/%s" % (self.app.config.pbs_instance_path, output_fname, self.app.config.pbs_dataset_server, self.app.config.pbs_dataset_path, output_fname)
+                    stageout += "%s@%s:%s" % (output_fname, self.app.config.pbs_dataset_server, output_fname)
                     # also stage in the empty output dataset files so the stageout doesn't fail when the tool outputs nothing
                     if stagein != '':
                         stagein += ','
-                    stagein += "%s/%s@%s:%s/%s" % (self.app.config.pbs_instance_path, output_fname, self.app.config.pbs_dataset_server, self.app.config.pbs_dataset_path, output_fname)
+                    stagein += "%s@%s:%s" % (output_fname, self.app.config.pbs_dataset_server, output_fname)
             job_attrs = pbs.new_attropl(4)
             job_attrs[0].name = pbs.ATTR_o
             job_attrs[0].value = pbs_ofile