Exemplo n.º 1
0
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()
Exemplo n.º 2
0
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()