CanDIG Server

This the documentation for version 1.4.0 of the candig-server.

The candig-server is a CanDIG project, and can be installed via pip install candig-server.

If you need help or want to report a bug, please refer to our Contribution Guideline

Setup

• Introduction
• Prepare Data For Ingestion
  • Clinical and Pipeline Metadata
  • Data Use Ontology
  • Reads, Variants and References Data
• Development Setup
  • Standalone candig-server Setup
  • Tyk and Keycloak Setup
• Production Deployment
  • Configuration file
  • Docker Deployment
  • Access List Setup
• Command Line Interface
  • Initialize/Remove Dataset
  • Add/Remove Clinical & Pipeline Metadata
  • Add/Remove Genomics Data
  • Other commands

Usage

• API Usage & Sample Queries
  • Sample queries for all metadata services
  • Sample queries for all variants services
  • Instructions for /search and /count endpoints

Appendix

• Contribution Guideline
  • GitHub workflow
• Status
  • Upgrade Guidelines