OGN Core Kit

OGN Core Kit is the open adoption surface for Omnis Genome Nexus (OGN).

It contains:

• Job Spec JSON v1 contract (spec/v1/jobspec.md + spec/v1/jobspec.schema.json + fixtures)
• ogn-runner: stable worker entrypoint that executes an OGN engine and uploads artifacts
• Python package ogn-sdk (CLI ogn, SDK ogn_sdk, runner ogn_runner)
• Workflow adapters (e.g. pipelines/ogn_variant.nf)

It does not include the proprietary OGN engine implementation, GPU kernels, or engine container images. The engine must be provided separately as a binary (e.g. ogn_run) or container image.

Install

Python (CLI + runner + SDK)

Requires Python 3.9+.

From PyPI:

python -m pip install ogn-sdk

From source (dev / editable):

python -m pip install -e sdk/python[dev]

This installs:

• ogn (CLI wrapper; requires access to an engine binary such as ogn_variant_runner)
• ogn-runner (worker entrypoint for Job Spec v1)
• ogn_sdk / ogn_runner Python modules

Rust (SDK)

The Rust crate lives at sdk/rust/ogn-sdk.

• If/when published, install via crates.io.
• Until then, consume it via a path dependency in a clone:

ogn-sdk = { path = "sdk/rust/ogn-sdk" }

Quickstart: ogn-runner (Job Spec v1)

ogn-runner accepts a jobspec path or - for stdin (the gateway worker contract is ogn-runner -).

Engine selection:

export OGN_ENGINE_BIN=/path/to/ogn_run
# or: ogn-runner -E /path/to/ogn_run job_spec.json

Run from a file:

ogn-runner job_spec.json

Run from stdin:

cat job_spec.json | ogn-runner -

Upload semantics

For each outputs.* artifact:

• If put_url is present, ogn-runner uploads via HTTP PUT to the presigned URL.
• Otherwise it uploads to uri directly when supported:
  • s3://... via aws s3 cp (AWS CLI required)
  • file://... or a plain path via a local copy

If an output is marked optional: true, upload failures are non-fatal.

Contracts

Canonical artifacts:

• spec/v1/jobspec.md
• spec/v1/jobspec.schema.json
• spec/v1/conformance/

Schema-level validation:

python tools/validate_conformance.py

Unknown fields are ignored (additive-only). Breaking changes require a new schema version (v2+).

Development

Run tests:

python -m pip install -e sdk/python[dev]
pytest -q

Public repo hygiene:

./public_audit.sh

License

Apache 2.0; see LICENSE and NOTICE.

Security

See SECURITY.md.

Contributing

See CONTRIBUTING.md.