Working inside a container

Rather than submitting commands from outside the container, alternatively you can work inside a container. This allows you to submit multiple commands one after another without the building and collapsing the container multiple times.

To make and enter a container, use:

singularity shell CONTAINER_NAME.sif

Substitute CONTAINER_NAME for the name of the container you wish to use.

Tip

  • Singularity links your entire HOME directory to the Singularity container. You can use ls to view the file system.

  • While working inside a container you can make new subdirectories (mkdir) to organise your outputs. These will persist after exiting the container.

  • To exit the container shell use the exit command. This will collapse the container.

Examples

To run build and enter a container named lolcow use:

singularity shell lolcow_latest.sif

You can now enter commands, for example:

cowsay -h

cowsay moo moo

cowthink -Tww Boo!

This is how the terminal will appear:

run cowsay inside container

  • singularity shell lolcow_latest.sif to make and enter the container,
  • Once inside the container the command prompt changes to Singularity>,
  • the command cowsay Boo! prints a cow saying 'Boo!',
  • exit is used to exit and collapse the container, and
  • the regular command prompt reappears .../RunAnyTool$.