From 698e2eb0e16ae7868ac4df46ec7c37739f76b83f Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Fri, 28 Sep 2007 21:17:43 +0000 Subject: [PATCH] Pathnames are now absolute, this broke the cluster staging. --- lib/galaxy/jobs/runners/pbs.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) 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