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Two new config vars to pull datasets from a server other than the

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application server.  When updating a cluster instance, the following
two new config vars must be set:

pbs_dataset_server = name-of-dataset-server
pbs_dataset_path = /path/to/datasets/on/dataset-server
This commit is contained in:
Nate Coraor
2007-03-16 06:30:39 +00:00
parent 15c38e5238
commit f5fcf39ff0
2 changed files with 5 additions and 3 deletions
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lib/galaxy/config.py
+2
View File
@@ -39,6 +39,8 @@ class Configuration( object ):
self.pbs_server = kwargs.get('pbs_server', "" )
self.pbs_instance_path = kwargs.get('pbs_instance_path', os.getcwd() )
self.pbs_application_server = kwargs.get('pbs_application_server', "" )
self.pbs_dataset_server = kwargs.get('pbs_dataset_server', "" )
self.pbs_dataset_path = kwargs.get('pbs_dataset_path', "" )
self.use_heartbeat = kwargs.get( 'use_heartbeat', False )
def get( self, key, default ):
return self.config_dict.get( key, default )
lib/galaxy/jobs/runners/pbs.py
+3 -3
View File
@@ -105,16 +105,16 @@ 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_application_server, os.getcwd(), input_fname)
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)
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_application_server, os.getcwd(), output_fname)
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)
# 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_application_server, os.getcwd(), output_fname)
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)
job_attrs = pbs.new_attropl(4)
job_attrs[0].name = pbs.ATTR_o
job_attrs[0].value = pbs_ofile