def main():
parser = getBasicOptionParser()
parser.add_argument(
"jobStore",
type=str,
help=("Store in which to place job management files \
and the global accessed temporary files"
"(If this is a file path this needs to be globally accessible "
"by all machines running jobs).\n"
"If the store already exists and restart is false an"
" ExistingJobStoreException exception will be thrown."))
parser.add_argument("--version", action='version', version=version)
options = parseBasicOptions(parser)
jobStore = loadJobStore(options.jobStore)
logger.info(
"Starting routine to kill running jobs in the toil workflow: %s" %
options.jobStore)
####This behaviour is now broken
batchSystem = loadBatchSystem(
jobStore.config
) #This should automatically kill the existing jobs.. so we're good.
for jobID in batchSystem.getIssuedBatchJobIDs(
): #Just in case we do it again.
batchSystem.killBatchJobs(jobID)
logger.info("All jobs SHOULD have been killed")
def main():
parser = getBasicOptionParser("usage: %prog [--jobStore] JOB_TREE_DIR [more options]", "%prog 0.1")
parser.add_option("--jobStore", dest="jobStore",
help="Job store path. Can also be specified as the single argument to the script.")
options, args = parseBasicOptions(parser)
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
assert len(args) <= 1 #Only toil may be specified as argument
if len(args) == 1: #Allow toil directory as arg
options.jobStore = args[0]
logger.info("Parsed arguments")
if options.jobStore == None:
parser.error("Specify --jobStore")
jobStore = loadJobStore(options.jobStore)
logger.info("Starting routine to kill running jobs in the toil workflow: %s" % options.jobStore)
####This behaviour is now broken
batchSystem = loadBatchSystem(jobStore.config) #This should automatically kill the existing jobs.. so we're good.
for jobID in batchSystem.getIssuedBatchJobIDs(): #Just in case we do it again.
batchSystem.killBatchJobs(jobID)
logger.info("All jobs SHOULD have been killed")
def main():
parser = getBasicOptionParser()
parser.add_argument("jobStore", type=str,
help=("Store in which to place job management files \
and the global accessed temporary files"
"(If this is a file path this needs to be globally accessible "
"by all machines running jobs).\n"
"If the store already exists and restart is false an"
" ExistingJobStoreException exception will be thrown."))
parser.add_argument("--version", action='version', version=version)
options = parseBasicOptions(parser)
jobStore = loadJobStore(options.jobStore)
logger.info("Starting routine to kill running jobs in the toil workflow: %s" % options.jobStore)
####This behaviour is now broken
batchSystem = loadBatchSystem(jobStore.config) #This should automatically kill the existing jobs.. so we're good.
for jobID in batchSystem.getIssuedBatchJobIDs(): #Just in case we do it again.
batchSystem.killBatchJobs(jobID)
logger.info("All jobs SHOULD have been killed")
