Pan Canadian Genome Library Data Access Compliance Office

Canada boasts world-leading expertise in genomics, including developing data-sharing policies and tools. However, we lack a national strategy to aggregate, store and share Canadian data equitably, securely and sustainably. At the same time, the size and complexity of human genomics datasets and their associated clinical data are growing rapidly.

The Pan-Canadian Genome Library (PCGL) is a large collaborative effort to unify Canada's genome sequencing efforts. The PCGL is an open-source and open-science initiative, building upon Canadian-made foundational components and datasets, and utilizing international standards such as GA4GH to unify Canada’s human genome sequencing efforts.

Repository Structure

The repository is organized with the following directory structure:

.
├── apps/
│   ├── ui
│   └── api
└── packages/
    ├── data-model
    ├── logger
    └── validation

Component	Package Name	Path	Description
DACO UI	@pcgl-daco/ui	apps/ui	React SPA website for PCGL Daco.
DACO API	@pcgl-daco/api	apps/api	ExpressJS backend-for-frontend server for
data-model	@pcgl-daco/data-model	packages/data-model	DACO database schemas and generated types.
logger	@pcgl-daco/logger	packages/logger	Standardized reusable logger and express middleware request logging.
validation	@pcgl-daco/validation	packages/validation	Shared type schemas for API and UI.

The modules in the monorepo are organized into two categories:

• apps/ - Standalone processes meant to be run. These are published to ghcr.io as container images.
• packages/ - Reusable packages shared between applications and other packages. Packages are published to NPM.

Local Development

Development Tools

• PNPM Project manager
• Node.js Runtime environment (v20 or higher)
• VS Code As recommended code editor. Plugins recommended: ESLint, Prettier - Code formatter, Mocha Test Explorer, Monorepo Workspace

System Dependencies

• This project uses Node ^20.9, Typescript ^5.5, and PNPM ^9.10, and was created using Vite 5.4.1.

Setup

Follow these steps to install and run all dependencies, then run all applications locally. The applications will run in development mode, monitoring the code base to rebuild and restart the applications when the code is updated.

• Install PNPM: npm i -g pnpm
• Install dependencies: pnpm i
• Run dependencies: docker-compose up -d
• Initialize application environment files: pnpm setup:all
  • This will fail if you have already made any .env files inside any of the /apps dirs. If this is the case, try removing these files before retrying the script.
  • This will also run the initial database migration for the DACO API, so make sure the docker dependencies are running.
• Start all apps in development mode: pnpm dev:all
  • The DACO API server will run at http://localhost:3000. Visit http://localhost:3000/api-docs for interactive swagger.
  • The UI will be running at http://localhost:5173

Support & Contributions

• Filing an issue