(options, stage, optionName)

(filename)

(command)

(name, options)

(self, jobID)

(msg, logger)

(stage, flag_file, *args)

(self)

(command)

(stage, comm, options)

(args)

()

(options)

(self)

()

(dir)

(self, stage, logDir='', verbose=0)

(stage, *args)

(options)

(path)

()

(self, jobID)

(self, qstat_max_tries = 5, qstat_error_delay = 1, qstat_delay = 10)

(self, command, walltime=None, name=None, memInGB=None, queue='batch', moduleList=None, logDi

(file, outputs)

(source, target)

(logDir, fullFilename, extension)

(file)

(files, outputs)

(file)