Introduction to Docker and Singularity

Introduction to Docker
8 Topics
Background about Docker
Docker components
Docker vocabulary
Container Setup explained
Basics of the Docker images
What is Containerization?
Advantages of Docker
Typical use cases
Using existing images
13 Topics
Explore Docker hub
Exercise on getting images
Get tools from Biocontainers
List docker images
Starting an image with docker run
Run container as daemon
Check containers status via docker ps
Clean up the containers and the images
Execute a process in running container
Summary
Volumes
Excercise with volumes
Ports
Docker recipes: build your own images
12 Topics
Building the recipes for images
More advanced image building
Building cache
Tagging the images
Starting the build
More instructions for the recipes
One tool, one image or some tools, one image
General recommendations
Dockerfile tips
Getting an image to Docker Hub
Inspecting Dockerfiles created by other parties
Using Biocontainers and Bioconda for bioinformatics tools
Introduction to Singularity
6 Topics
Background about Singularity
Strengths and Weaknesses
Singularity Architecture
Getting started
Singularity’s Image Cache
Using existing Singularity images
Run and execute Singularity images
6 Topics
Using the Singularity containers to run commands
Files in Singularity containers
Binding local folders (aka volumes)
Using Docker images with Singularity
Run from sandbox container or remotely
Troubleshooting options
Building Singularity images
4 Topics
Building Singularity images
Change the image via sandbox
Using singularity recipes
Remotely building
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Advantages of Docker

Introduction to Docker and Singularity Introduction to Docker Advantages of Docker

Distributing and using software as a Docker image gives you:

  • Bundled Dependencies – Docker images contain all their own dependencies, which means you don’t have to do any installation yourself (compared to an application that is just source code or a .deb installer)
  • Cross-platform Installation – Docker containers contain their own operating system, so they will run on any platform (even Windows!)
  • Easy Distribution – Can be distributed as a single .tar image file, or put on docker hub so it can be docker pull‘d
  • Safety – Files in a container can’t access files on the host machine, so users can trust dockerized applications
  • Ease-of-Use – Docker containers can always be run using one single docker run command
  • Easy Upgrades – Docker containers can be easily swapped out for newer versions, while all persistent data can be retained in a data volume
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