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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Getting started

Introduction to Docker and Singularity Introduction to Singularity Getting started

Singularity is another container platform. In some ways it appears similar to Docker from a user perspective, but in others, particularly in the system’s architecture, it is fundamentally different. These differences mean that Singularity is particularly well-suited to running on distributed, High Performance Computing (HPC) infrastructure, as well as a Linux laptop or desktop!

System administrators will not, generally, install Docker on shared computing platforms such as lab desktops, research clusters or HPC platforms because the design of Docker presents potential security issues for shared platforms with multiple users. Singularity, on the other hand, can be run by end-users entirely within “user space”, that is, no special administrative privileges need to be assigned to a user in order for them to run and interact with containers on a platform where Singularity has been installed.

On our training servers you will be able to use sudo to build singularity images whereas on the HPC of the VSC (Flemish Super Computer) some limitations are present (see section 26 http://hpcugent.github.io/vsc_user_docs/pdf/intro-HPC-linux-gent.pdf)

Sign in to the remote platform, with Singularity installed, that you’ve been provided with access to. Check that the singularity command is available in your terminal.

singularity --version

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