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• Singularity Pull
• Singularity Shell

Singularity Pull

We have covered creating a docker image and pushing it to Dockerhub. Next, we can use Singularity to pull the image locally, creating an executable container.

This is a slightly obtuse way of creating containers - utilising both Docker and Singularity - however in my opinion pushing images to dockerhub comes with benefits:

1. Automatic linting on Dockerhub to test the stability of the image.
2. Link to github repository, can deploy automatic triggers when a commit is made to the repository.
3. Reduces the storage requirements of the container.

To pull a docker container, use the following singularity command specifying the name of the image to create and the Dockerhub repostiory to pull from:

singularity pull --name week1.img docker://USERNAME/REPO:TAG

You will now have created an image called week1.img.

Singularity shell

To ‘enter’ the container interactively and to utilise its tools, use the singularity shell command:

singularity shell -B $(pwd) week1.img

The -B prefix specifies the bind path. Once inside the container, the container cannot “see” files that are in directories above the bind path specified. We used $(pwd) which is the same as the current directory path.

To Do:

1. Enter the container
2. Check that fastqc, multiqc and bbduk.sh all work.
3. Use whereis to print the path of each tool within the container. Can you see where conda installed the environment?
4. Exit the container.