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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Troubleshooting options

Introduction to Docker and Singularity Run and execute Singularity images Troubleshooting options

Fakeroot

Singularity permissions are an evolving field. If you don’t have access to sudo, it might be worth considering using –fakeroot/-f parameter.

Singularity cache directory

$HOME/.singularity
  • It stores cached images from registries, instances, etc.
  • If problems may be a good place to clean. When running sudo, $HOME is /root.

Global singularity configuration

Normally at /etc/singularity/singularity.conf or similar (e.g preceded by /usr/local/)

  • It can only be modified by users with administration permissions
  • Worth noting bind path lines, which point default mounted directories in containers
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