Introduction to Docker and Singularity

Introduction to Docker
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
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
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
Background about Singularity
Strengths and Weaknesses
Singularity Architecture
Getting started
Singularity’s Image Cache
Using existing Singularity images
Run and execute Singularity images
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
Building Singularity images
Change the image via sandbox
Using singularity recipes
Remotely building
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Excercise with volumes

Introduction to Docker and Singularity Using existing images Excercise with volumes
  1. Mount the data directory with the four fastq files from available datasets in Github repository
  2. Run fastqc interactively (inside container): e.g. fastqc /course/*.gz
  3. Run fastqc from your host using the running or a freshly started container
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