def main():
'''Initialise the pipeline, then run it'''
# Parse command line arguments
options = parse_command_line()
# Initialise the logger
logger = Logger(__name__, options.log_file, options.verbose)
# Log the command line used to run the pipeline
logger.info(' '.join(sys.argv))
drmaa_session = None
try:
# Set up the DRMAA session for running cluster jobs
import drmaa
drmaa_session = drmaa.Session()
drmaa_session.initialize()
except Exception as e:
print("{progname} error using DRMAA library".format(
progname=program_name),
file=sys.stdout)
print("Error message: {msg}".format(msg=e.message, file=sys.stdout))
exit(error_codes.DRMAA_ERROR)
# Parse the configuration file, and initialise global state
config = Config(options.config)
config.validate()
state = State(options=options,
config=config,
logger=logger,
drmaa_session=drmaa_session)
# Build the pipeline workflow
pipeline = make_pipeline(state)
# Run (or print) the pipeline
cmdline.run(options)
if drmaa_session is not None:
# Shut down the DRMAA session
drmaa_session.exit()
def main():
'''Initialise the pipeline, then run it'''
# Parse command line arguments
options = parse_command_line()
# Initialise the logger
logger = Logger(__name__, options.log_file, options.verbose)
# Log the command line used to run the pipeline
logger.info(' '.join(sys.argv))
drmaa_session = None
try:
# Set up the DRMAA session for running cluster jobs
import drmaa
drmaa_session = drmaa.Session()
drmaa_session.initialize()
except Exception as e:
print("{progname} error using DRMAA library".format(progname=program_name), file=sys.stdout)
print("Error message: {msg}".format(msg=e.message, file=sys.stdout))
exit(error_codes.DRMAA_ERROR)
# Parse the configuration file, and initialise global state
config = Config(options.config)
config.validate()
state = State(options=options, config=config, logger=logger,
drmaa_session=drmaa_session)
# Build the pipeline workflow
pipeline = make_pipeline(state)
# Run (or print) the pipeline
cmdline.run(options)
if drmaa_session is not None:
# Shut down the DRMAA session
drmaa_session.exit()
def main():
'''Initialise the pipeline, then run it'''
# Parse command line arguments
options = parse_command_line()
# Initialise the logger
logger = Logger(__name__, options.log_file, options.verbose)
# Log the command line used to run the pipeline
logger.info(' '.join(sys.argv))
# Set up the DRMAA session for running cluster jobs
drmaa_session = drmaa.Session()
drmaa_session.initialize()
# Parse the configuration file, and initialise global state
config = Config(options.config)
config.validate()
state = State(options=options, config=config, logger=logger,
drmaa_session=drmaa_session)
# Build the pipeline workflow
pipeline = make_pipeline(state)
# Run (or print) the pipeline
cmdline.run(options)
# Shut down the DRMAA session
drmaa_session.exit()
def main():
'''Initialise the pipeline, then run it'''
# Parse command line arguments
options = parse_command_line()
# Initialise the logger
logger = Logger(__name__, options.log_file, options.verbose)
# Log the command line used to run the pipeline
logger.info(' '.join(sys.argv))
# Set up the DRMAA session for running cluster jobs
drmaa_session = drmaa.Session()
drmaa_session.initialize()
# Parse the configuration file, and initialise global state
config = Config(options.config)
config.validate()
state = State(options=options,
config=config,
logger=logger,
drmaa_session=drmaa_session)
# Build the pipeline workflow
pipeline = make_pipeline(state)
# Run (or print) the pipeline
cmdline.run(options)
# Shut down the DRMAA session
drmaa_session.exit()