Singularity

Why use both Docker and Singularity?

Singularity can be thought of as the bona fide ‘open source’ container platform, and offers some advantages over Docker:

• Singularity does not require sudo privelages. This means we can run Singularity on HPC/cloud platforms.

• Singularity is compatible with Docker i.e we can pull images from Dockerhub using Singularity.

The main reason we are using Docker is that it is compatitble with Github actions (CI testing).

Singularity pull

On your local machine, pull the docker image we created in the previous step:

$ singularity pull --name test.img docker://USERNAME/test

The container test.img should be present in your directory. Shell into the container:

$ singularity shell -B $(pwd) test.img

Note

The -B flag indicates the bind path for the container. Your container will not be able to access files above $(pwd) in the directory tree.

Confirm the installation path of fastqc within the container:

$ whereis fastqc