Working with Docker

Docker technology has revolutionized reproducibility by creating a fast, portable, easily shareable method to generate the exact compute environment, with all dependencies and configurations, that were used to run a tool or workflow.

Below, we provide resources for finding public Docker images or creating your own image to use with your analysis. Docker is commonly used by software engineers, and learning material on the internet may be overly complex for the researcher use case. We compiled learning materials from each platform within BioData Catalyst to help you get started using Docker specifically for bioinformatics pipelines.

Available Docker images

We highly recommend users begin with an official or maintained image (for example, from BioContainer) to ensure you are using secure software.

• Official Images

• UW-GAC TOPMed

• BioContainer maintains images for 1K+ bioinformatics tools

Introductory learning material

Below, we have compiled learning resources from various sources to help you get started learning Docker:

• Best Practices for Writing Dockerfiles

• Build Context tips

• Dockstore’s Getting Started with Docker

• Terra

  • Install Docker and test that it works

  • Publish a Docker container to Google Container Registry

  • Make a Docker container the easy way

  • Making a safe and secure custom Docker image

• Seven Bridges

  • Docker basics

  • Install Docker

  • BioData Catalyst Image Registry

  • Manage Docker repositories