Building Singularity images
Introduction
As a platform that is widely used in the scientific/research software and HPC communities, Singularity provides great support for reproducibility. If you build a Singularity image for some scientific software, it’s likely that you and/or others will want to be able to reproduce exactly the same environment again. Maybe you want to verify the results of the code or provide a means that others can use to verify the results to support a paper or report. Maybe you’re making a tool available to others and want to ensure that they have exactly the right version/configuration of the code.
Similarly to Docker and many other modern software tools, Singularity follows the “Configuration as code” approach and a container configuration can be stored in a file which can then be committed to your version control system alongside other code. Assuming it is suitably configured, this file can then be used by you or other individuals (or by automated build tools) to reproduce a container with the same configuration at some point in the future.
Different approaches to building images
There are various approaches to building Singularity images. We highlight two different approaches and focus on one of them:
- Building within a sandbox: You can build a container interactively within a sandbox environment. This means you get a shell within the container environment and install and configure packages and code as you wish before exiting the sandbox and converting it into a container image.
- Building from a Singularity Definition File: This is Singularity’s equivalent to building a Docker container from a
Dockerfileand we’ll discuss this approach in this section.
You can take a look at Singularity’s “Build a Container” documentation for more details on different approaches to building containers.
As soon as you need to build an image, you’d need to start a job on the cluster.
Build from Registries
- Docker Hub
https://hub.docker.com/r/biocontainers/fastqc
singularity build fastqc-0.11.9_cv7.sif docker://biocontainers/fastqc:v0.11.9_cv7
- Biocontainers
Via quay.io
https://quay.io/repository/biocontainers/fastqc
singularity build fastqc-0.11.9.sif docker://quay.io/biocontainers/fastqc:0.11.9--0
Via Galaxy project prebuilt images
singularity pull --name fastqc-0.11.9.sif https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0
- Docker Daemon (local Docker image)
singularity build fastqc-web-0.11.9.sif docker-daemon://fastqc-0.11.9--0
- Also Singularity registries (not so popular so far)