This container is meant to encapsulate BIDS App containers for execution with AWS roles and S3 inputs/outputs. It must be run with the options --privileged -v /var/run/docker.sock:/var/run/docker.sock
to start containers on the host.
- BIDS_ANALYSIS_ID: A unique key for a combination of dataset and parameters
- BIDS_CONTAINER: path:tag for BIDS app container
- BIDS_DATASET_BUCKET: S3 Bucket containing BIDS directories
- BIDS_OUTPUT_BUCKET: Writable S3 Bucket for output
- BIDS_SNAPSHOT_ID: The key to reference which BIDS directory
- BIDS_ANALYSIS_LEVEL: Select for participant, group, etc
- BIDS_ARGUMENTS: Optionally any additional parameters required
These are mostly useful for debugging.
- DISABLE_PRUNE: Prevents the container from removing images/volumes
- AWS_ACCESS_KEY_ID: Optionally use these credentials with S3
- AWS_SECRET_ACCESS_KEY: Optionally use these credentials with S3
If no S3 credentials are provided, the EC2 instance role is used.