GKM Starter Kit

A practical entry point for using the GA4GH Genomic Knowledge Model (GKM).

Live site: https://ga4gh.github.io/gkm-starter-kit/

The Starter Kit brings together three complementary resources:

• Data Bundles package related GKM objects from participating producers.
• ga4gh.gkm provides Python tools for loading and working with those bundles.
• Vignettes show how implementers use GKM standards to solve real problems.

Start with the documentation for an overview, examples, and API details.

Contributing a vignette

1. Read the contribution guide on the live site.
2. Either:
   • Open a Propose a vignette issue, or
   • Copy docs/vignettes/_template/vignette.md into a new docs/vignettes/<slug>/ folder, fill it in, and open a PR.

ga4gh.gkm Python package

Installation

Install from PyPI:

python3 -m pip install ga4gh.gkm

Development

Clone the repo and create a virtual environment:

git clone https://github.com/ga4gh/gkm-starter-kit
cd gkm-starter-kit
python3 -m venv venv
source venv/bin/activate

Install development dependencies and prek:

python3 -m pip install -e '.[dev,tests,docs,notebooks]'
prek install

Check style with ruff:

python3 -m ruff check .
python3 -m ruff format --check .

Run tests with pytest:

pytest

Docs

python -m scripts.build_docs
zensical serve

Then open http://127.0.0.1:8000.

License

CC0 1.0 Universal