Using Docker

Why Docker?

• Portability - Run code and scripts on any machine that has Docker installed

  • Avoids installation headaches on multiple machines (dependencies are installed with software)

  • Make it easy to run batch jobs on multiple instances

• Reproducibility - be able to run code and generate the same outputs given a set of input files

  • Tie all software to specific versions

  • Utilize Docker images with multiple bioinformatics software installed

  • Examples: Rocker Project, GATK4

Docker Terms

• Docker Registries

  • Collection of repositories that hold container images

  • docker pull: pulls the images from a registry to a container on our machine

  • docker commit: When we commit changes, these changes are saved to the image in registry

Snapshots vs Images on the Platform

There are hard limits for using Docker Images.

• DockerHub and other registries have a pull limit of 200 pulls/user/day

• Saving a snapshot file to your project lets you scale without these limits

• Especially helpful in batch processing

Docker and Security

• Use images from trusted vendors whenever possible

  • Examples: Official Ubuntu Image, Amazon Linux Image, Biocontainers

  • Avoid "kitchen sink" images - hard to manage vulnerabilities

• In general: pay attention to possible vulnerabilities and whether they affect your containers

• Use dockerfiles to uninstall/patch possible vulnerabilities in images

Resources

Full Documentation

To create a support ticket if there are technical issues:

1. Go to the Help header (same section where Projects and Tools are) inside the platform

2. Select "Contact Support"

3. Fill in the Subject and Message to submit a support ticket.