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Bug in SGE external metadata

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Nate Coraor
2010-05-10 11:22:50 -04:00
parent 273861ace3
commit ac033db509
1 changed files with 1 additions and 2 deletions
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lib/galaxy/jobs/runners/sge.py
+1 -2
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@@ -166,12 +166,11 @@ class SGEJobRunner( object ):
script = sge_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line)
if self.app.config.set_metadata_externally:
output_fnames = [ str( o ) for o in job_wrapper.get_output_fnames() ]
script += "cd %s\n" % os.path.abspath( os.getcwd() )
script += "%s\n" % job_wrapper.setup_external_metadata( exec_dir = os.path.abspath( os.getcwd() ),
tmp_dir = self.app.config.new_file_path,
dataset_files_path = self.app.model.Dataset.file_path,
output_fnames = output_fnames,
output_fnames = job_wrapper.get_output_fnames(),
set_extension = False,
kwds = { 'overwrite' : False } ) #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior
fh = file( jt.remoteCommand, "w" )