vlln/bio-skills/biocontainers

Biocontainers Skill

Query the BioContainers Registry through the GA4GH Tool Registry Service (TRS) API.

Trigger Keywords

• Domain terms: biocontainers, BioContainers, bioinformatics container, containerized bioinformatics tool
• Image references: quay.io/biocontainers, bioinformatics Docker image
• API terms: GA4GH TRS, TRS API, Tool Registry Service
• Workflow: find bioinformatics tool container, look up container version, resolve image tag

Capabilities

Workflow

1. Search first when the exact BioContainers tool name is uncertain.
2. Inspect a tool for registry metadata and the latest version summary.
3. Inspect a specific version when the user needs full quay.io/biocontainers/… image tags.
4. List versions when the user only needs available upstream versions.

Prefer inspecting a specific version over listing versions when the final answer needs a runnable image reference.

Gotchas

• Version tags include build hashes. A BioContainers image tag is not just a semantic version — it uses the format <version>--<build> (e.g., 0.7.17--h5bf99c6_12). The -- separator is part of the BioContainers convention.
• Multiple entries per tool. Some tools have separate BioContainers entries from different conda channels. When a search returns multiple plausible tools, present the ambiguity and let the user choose.
• API version. The BioContainers API follows GA4GH TRS v2, not v1. Endpoints and response schemas differ.
• API base URL. The default endpoint is https://api.biocontainers.pro/ga4gh/trs/v2. Override with BIOCONTAINERS_API_URL only when necessary.
• Not for Docker Hub. BioContainers images live on quay.io, not Docker Hub. Do not use this skill for generic Docker Hub searches or for running containers locally.

Output

Summarize the matching tool, relevant versions, and the exact image tag or command the user can use next. Report full quay.io/biocontainers/… tags exactly as returned by the API. Include uncertainty when a search returns multiple plausible tools.