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()
