Input

Build and Run Commands

Local or AWS

git clone https://github.com/SWOT-Confluence/metroman.git

cd metroman

docker build -t metroman .

docker run -e AWS_BATCH_JOB_ID=”foo” -v /mnt/input:/mnt/data/input travissimmons/metroman:latest -r metrosets.json -s local -v -i 0

HPC

singularity build metroman.simg docker://travissimmons/metroman

singularity run –env AWS_BATCH_JOB_ID=”foo” –bind mnt/input:/mnt/data/input,mnt/flpe/metroman:/mnt/data/output metroman.simg -i 0 -r metrosets.json -s local -v

Arguments

def create_args(): “"”Create and return argparsers with command line arguments.”””

arg_parser = argparse.ArgumentParser(description='Integrate FLPE')
arg_parser.add_argument('-i',
                        '--index',
                        type=int,
                        default = -235,
                        help='Index to specify input data to execute on')
arg_parser.add_argument('-r',
                        '--reachjson',
                        type=str,
                        help='Name of the reach.json',
                        default='metrosets.json')
arg_parser.add_argument('-v',
                        '--verbose',
                        help='Indicates verbose logging',
                        action='store_true')
arg_parser.add_argument('-s',
                        '--sosbucket',
                        type=str,
                        help='Name of the SoS bucket and key to download from',
                        default='')
return arg_parser

Dev notes….