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Pathnames are now absolute, this broke the cluster staging.

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Nate Coraor
2007-09-28 21:17:43 +00:00
parent 19d06f68a0
commit 698e2eb0e1
1 changed files with 4 additions and 3 deletions
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lib/galaxy/jobs/runners/pbs.py
+4 -3
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@@ -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