BGC Viewer

A viewer for biosynthetic gene cluster (BGC) data.

Installation & run

Using Python 3.11 or higher, install and run the BGC Viewer as follows:

pip install bgc-viewer
bgc-viewer

This will start the BGC Viewer server, to which you can connect with your web browser.

Configuration

Environment variables can be set to change the configuration of the viewer. A convenient way to change them is to put a file called .env in the directory from which you are running the application.

Basic Configuration

BGCV_HOST=localhost       # Server host (default: localhost)
BGCV_PORT=5005            # Server port (default: 5005)
BGCV_DEBUG_MODE=False     # Enable dev/debug mode (default: False)

Public Mode (Multi-user Deployment)

BGCV_PUBLIC_MODE=True                         # Enable public mode
BGCV_DATABASE_PATH=/path/to/attributes.db     # Path to index database file (required)
BGCV_SECRET_KEY=your-secret-key               # Secret key for session signing (required)
REDIS_URL=redis://localhost:6379              # Redis URL for session storage (recommended)
HTTPS_ENABLED=True                            # Enable secure cookies for HTTPS
BGCV_ALLOWED_ORIGINS=https://yourdomain.com   # Allowed CORS origins

In public mode:

The database path points to an attributes.db index file
The actual data location (data_root) is read from the database metadata
Multiple users can access the application simultaneously with session support
File system browsing and preprocessing endpoints are disabled

For more configuration options, see .env.example.

Development

See the repository main README for development details.

uv run python -m bgc_viewer.app

License

Apache 2.0

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