ClinGen Tools

Production Site | Test Site

ClinGen Tools is one Django web application that houses the internal tools the Stanford ClinGen team builds and maintains. Keeping the tools in one application means one codebase, one set of dependencies, one server, and one deployment to look after, instead of one of each per tool.

• Affiliations Service (AS), at /as/: the source of truth for ClinGen affiliations (expert panels and working groups), with a REST API for other ClinGen tools and a UI for ClinGen staff.
• ClinVar Submission Service (CSS), at /css/: accepts ClinVar submissions from ClinGen clients through an API, forwards them to ClinVar, and tracks each one until ClinVar has processed it.
• Email Transfer Service (ETS), at /ets/: moves a GCI/VCI user's account from an old email to a new one.

The landing page at tools.clinicalgenome.org links to each tool. docs/design.md describes the design.

ClinGen Tools is maintained by the Stanford contingent of ClinGen.

Getting Started

• Install uv.
• Install Node.js (see .nvmrc for the version).
• Install just.
• Install bd (Beads), which we use to track work.
• Clone the repository.
• Install JavaScript dependencies: npm ci.
• Install Python dependencies: uv sync.
• Copy .env.example to .env in the root of the repository and fill in the values. When you add or remove a key, change both files; just env-check reports any differences.
• Build the static assets: just js-build.
• Apply migrations: just django-migrate.
• Run the development server: just django-runserver.

Run just --list to see every recipe. docs/how-to.md covers infrastructure and deployment.

Contributing

You are welcome to submit a bug report or a pull request.