Docker

Docker is not available on SciNet's clusters. However, you can use singularity to run docker images.

Fetching a docker image

$ singularity pull docker://alpine:latest

This pulls the alpine:latest image from Docker Hub and converts it to singularity's image format, saving it as a file named alpine_latest.sif.

As this requires an internet connection to work, it can only be done on the login nodes, and not in job scripts.

You can also pull from other docker registries, e.g.:

 $ singularity pull docker://quay.io/biocontainers/samtools:1.13--h8c37831_0

This creates an image file named samtools_1.13--h8c37831_0.sif.

Running a command inside the image

$ singularity exec alpine_latest.sif cat /etc/alpine-release
3.14.0

$ singularity exec samtools_1.13--h8c37831_0.sif samtools --version
samtools 1.13
Using htslib 1.13
...