Input
Build and Run Commands
Local or AWS
git clone https://github.com/SWOT-Confluence/neobam.git
cd neobam
docker build -t neobam .
docker run -v /mnt/input:/mnt/data/input -v /mnt/flpe/geobam:/mnt/data/output neobam -i 1 -r reaches.json
HPC
singularity build neoobam.simg docker://travissimmons/neobam
singularity run –bind mnt/input:/mnt/data/input,mnt/flpe//geobam:/mnt/data/output neobam.simg -i 1 -r reaches.json
Arguments
””” option_list <- list( make_option(c(“-i”, “–index”), type = “integer”, default = NULL, help = “Index to run on”), make_option(c(“-b”, “–bucket_key”), type = “character”, default = “”, help = “Bucket key to find the sos”), make_option(c(“-r”, “–reaches_json”), type = “character”, default = “reaches.json”, help = “Name of reaches.json”) ) “””