def run(): # get options and defaults options = getOptions() grid = GridEngine(options.logFileFilePath) try: # create Grid Engine class print "reading job info" # get a dictionary of class jobs for all jobs to be run JobsDict = {} JobVariables = { "$InputsFolder": options.inputFolder, "$OutputsFolder": options.outputFolder, "$JobOutputFolder": options.jobOutputFolder, "$JobErrorFolder": options.jobErrorFolder, "$ScriptPath": options.jobScriptFolder, } # run all jobs RunJobs(JobsDict, grid, options.csvFile, options.statusFolder, options.VariablesFile, JobVariables) finally: # exit drmaa session if grid: grid.exit()
def run(): # get options and defaults options = getOptions() grid = GridEngine(options.logFileFilePath) try: # create Grid Engine class print "reading job info" # get a dictionary of class jobs for all jobs to be run JobsDict = parsePipelineInfoFile(options.JobInfoFile, options.VariablesFile, grid) # run all jobs RunJobs(JobsDict, grid) finally: # exit drmaa session if grid: grid.exit()