Developers

For Developers

Write a YAML recipe, push it through the Hub CI, and your tool ends up signed in registry.biochef.app and runnable from the BioChef web app.

Quickstarts

Three ways in

Pick a path and get to a running BioChef in under five minutes.

Step 01 · Author

Write a new recipe

Author a YAML recipe in your own repo. The Hub workflow validates, signs, and publishes it for you.

  1. 1 Fork biochef-recipes and create recipes/<tool>/biochef.yaml.
  2. 2 Run hub validate and add tiny golden fixtures under tests/.
  3. 3 Open a PR. The reusable Hub workflow runs validate → build → SBOM → cosign → publish.
Hub setup guide

Step 02 · Run

Run the BioChef app locally

Clone the SPA, install deps, and serve it with the dev server. No backend required.

  1. 1 git clone https://github.com/ieeta-pt/Biochef and npm install.
  2. 2 (Optional) install Emscripten 3.1.65 and run npm run build-wasm to rebuild WASM modules from source.
  3. 3 npm start and open http://localhost:8082.
ieeta-pt/Biochef

Step 03 · Inspect

Pull a signed bundle

Tools live in the BioChef Registry as content-addressable OCI bundles. The web app fetches them by digest at runtime; you can pull and verify them locally with the Hub CLI or ORAS.

  1. 1 Resolve a tool by digest in the signed index.json.
  2. 2 Pull the OCI bundle (bundle.json + WASM/JS layers + SBOM) with the Hub CLI or ORAS.
  3. 3 Verify the cosign signature before loading the tool.
Hub CLI on GitHub

Snippets

What the code looks like

A recipe in YAML, the Hub CLI run, and a saved workflow.

name: aligner
version: 1.0.0
inputs:
  - id: reads
    type: File
    format: fastq
steps:
  - id: qc
    uses: biochef/qc@1.2.0
  - id: align
    uses: biochef/bwa@0.7
outputs:
  - id: bam
    from: align
yaml14 lines