poldracklab/bids-app-host repository overview

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.

⁠Required environment variables/configuration:

• 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

⁠Optional environment variables

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.