A container is an application bundled together with its dependencies and a minimal operating system.

Singularity is a container platform that is generally preferred over Docker for HPC applications due to security concerns. (Singularity runs container images under the user’s limited access permissions, whereas Docker allows root access).

Singularity User Guide

First steps

  • Download a singularity image (lolcow_latest.sif): 
    singularity pull library://lolcow
  • Enter a shell inside the container: 
    singularity shell lolcow_latest.sif
  • Run a container image: 
    singularity run lolcow_latest.sif
  • Execute a command from inside the container: 
    singularity exec lolcow_latest.sif date
  • Pull a docker container: 
    # docker pull biocontainers/blast:2.2.31
singularity pull docker://biocontainers/blast:2.2.31