daylily-omics-references

Bash utilities for creating and validating the reference S3 buckets used by daylily-ephemeral-cluster. The project now ships a single shell script that wraps AWS CLI commands to clone public reference data, validate an existing bucket, or ensure a bucket exists and matches the expected structure.

The commands shell out to the AWS CLI for recursive S3 copy operations. Ensure that the AWS CLI and jq are installed and that your environment is authenticated before running the script.

Usage

The entry point lives at scripts/daylily-omics-references.sh. Global options may be placed before the subcommand.

Usage: daylily-omics-references.sh [GLOBAL OPTIONS] <command> [ARGS]

Global options:
  --profile PROFILE   AWS profile to use
  --region REGION     AWS region to target (required for clone/ensure)

Commands:
  clone   Create a new reference bucket from the public source
  verify  Validate that a bucket matches the expected structure
  ensure  Verify a bucket or create it if missing

Clone a new reference bucket

scripts/daylily-omics-references.sh \
  --profile daylily-service \
  clone \
  --bucket-prefix myorg \
  --region us-west-2 \
  --execute

This creates myorg-omics-analysis-us-west-2, enables transfer acceleration and copies the default reference version (0.7.131c). Use --exclude-hg38, --exclude-b37, or --exclude-giab to omit large subsets. Pass --use-acceleration to copy via the S3 accelerate endpoint.

Verify an existing bucket

scripts/daylily-omics-references.sh \
  --profile daylily-service \
  verify \
  --bucket myorg-omics-analysis-us-west-2

This validates that the bucket exists, contains the expected folder structure and that its s3_reference_data_version.info marker matches the default version.

Ensure a bucket is ready for daylily-ephemeral-cluster

scripts/daylily-omics-references.sh \
  --profile daylily-service \
  ensure \
  --bucket-prefix myorg \
  --region us-west-2 \
  --execute

The command verifies the bucket when it already exists; otherwise it creates the bucket using the same cloning logic.

Development

The repository now consists solely of the bash script above. No Python dependencies are required. If you modify the script, ensure it remains POSIX shell compatible and keep the usage examples up to date.