Bonsai

Bonsai is a web app for visualising the output from the bacterial analysis pipeline jasen as well as performing cluster analysis, annotation, and more. Bonsai is a multi-user application for collaborating on analysing outbreaks and antibiotic resistance of human pathogenic bacteria.

Note

Bonsai is under active development and in alpha stage. Expect limited documentation, breaking changes, and bugs until the official 1.0 release.

Check out the Installation section for installation instructions.

• Installation
  • Setup Bonsai with docker-compose
  • Create database indexes
  • Create an admin user
  • Setup IGV integration
  • Accessing the web interface
  • Upload samples to Bonsai
  • Data persistance
• Configuring Bonsai
  • Ports
  • Environmental variables
  • Volume mappings
  • Specific configuration files
• Administration
  • Index database
  • Create users
  • Upload samples
  • Create and manage groups of samples
• Deployment into a production environment
• LIMS Export — Configuration & Usage
  • Overview
  • Configuration Schema (YAML)
  • How the Export Works
  • Built-in Formatters
  • API Usage
  • CLI Usage
  • Serialization Details
  • Error Semantics (Summary)
  • Extending the System
  • Best Practices
• Frequently asked questions