Singularity-in-Docker

This repository stores a simple setup for getting Singularity inside a Docker image. The main use-case for this is when you have Docker on your local computer but want to run an image on a computer cluster (such as Uppmax), for example Mac users. This setup should only be used for building Singularity images, not running them!

Setup

The first thing you need to do is to create the Docker image containing Singularity:

docker build -f Dockerfile -t singularity-in-docker .

Building from Docker images

The main use-case here is building a Singularity image from a local Docker image. Start by creating your Dockerfile and building your image, just like you normally would. You then need to save your image to a tarball:

docker save <IMAGE ID> -o docker.tar

The <IMAGE ID> must be the exact ID that you see when you list your images with docker image ls, you cannot use e.g. ubuntu:latest or similar repository:tag pairs. You can now mount and build your Singularity image from the saved tarball:

docker run -v $(pwd):/work singularity-in-docker \
    build my-image.sif docker-archive://docker.tar

Building from definition files

You can also build images from Singularity definitions files like normal:

docker run --privileged -v $(pwd):/work singularity-in-docker \
    build my-image.sif my-image.def

Troubleshooting

If you run into a wget: unable to resolve host address 'github.com' error on Mac OSX, try updating your Docker installation.