Setfinder

Build and Run Commands

Local or AWS

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

cd setfinder

docker build -t setfinder .

or

docker pull travissimmons/setfinder:latest

Expanded docker run -v /mnt/input:/data setfinder -r reaches_of_interest.json -c continent-setfinder.json -e -s 16 -o /data -a MetroMan HiVDI SIC NeoBAM -e -n /data -i 3

Not Expanded docker run -v /mnt/input:/data setfinder -r reaches_of_interest.json -c continent-setfinder.json -e -s 16 -o /data -a MetroMan HiVDI SIC NeoBAM -n /data -i 3

HPC

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

singularity run –bind mnt/input:/data setfinder.simg -r reaches_of_interest.json -c continent.json -e -s 16 -o /data -n /data -a MetroMan HiVDI SIC NeoBAM -i 0

Arguments

def get_args(): “"”Get command-line arguments”””

parser = argparse.ArgumentParser(
    formatter_class=argparse.ArgumentDefaultsHelpFormatter)

parser.add_argument('-i',
                    '--index',
                    help='Index that indicates what continent to run on',
                    metavar='index',
                    type=int)

parser.add_argument('-a',
                    '--algorithms',
                    help='A list of algorithm names',
                    nargs='+')

parser.add_argument('-e', 
                    '--expanded', 
                    action='store_true', 
                    help='Expanded mode')

parser.add_argument('-n',
                    '--indir',
                    help='Path to input directory',
                    metavar='indir',
                    type=str)

parser.add_argument('-o',
                    '--outdir',
                    help='Path to output directory',
                    metavar='outdir',
                    type=str)

parser.add_argument('-s',
                    '--sword_version',
                    help='Sword version number',
                    metavar='sword_version',
                    type=int)

parser.add_argument('-g', 
                    '--globalrun', 
                    action='store_true', 
                    help='Global execution so load reaches from SWORD')

parser.add_argument("-c",
                    "--jsonfile",
                    type=str,
                    help="Name of continent JSON file",
                    default="continent.json")

parser.add_argument("-r",
                    "--reachsubset",
                    type=str,
                    help="Name of reach subset file")

return parser.parse_args()

Dev notes….