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CellProfiler / BatchProfiler

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Directories not properly escaped in qsub #7

Closed LeeKamentsky closed 8 years ago

LeeKamentsky commented 8 years ago

Directory names and other parameters are specified without quotes on the command-line. The parameters need to be properly quoted and escaped. For instance, a directory name of "/foo - bar" will yield the error message:

<type 'exceptions.RuntimeError'>: Failed to submit job: qsub: ERROR! invalid option argument "-" 
  args = ('Failed to submit job: qsub: ERROR! invalid option argument "-"\n',) 
  message = 'Failed to submit job: qsub: ERROR! invalid option argument "-"\n'