Docker and Apptainer

To run a docker image using docker:

docker run -it --rm <image> command

where:

• -it: Lets you interact with the container as if it was a shell
• --rm: Automatically remove the container when it exits.
• command: a command to run within the container, typically bash

Mounting a local directory on the container for permanent storage can be achieved using the -v binding. For example this will have the local ~/mywork available on the container in /usr/local/mywork:

docker run -it --rm  -v ~/mywork:/usr/local/mywork <image> command

Useful commands

The dockerfile keyworkd CMD can point to a script that will run if the docker run command flag is not included.

The keyworkd ENTRYPOINT defines a script that will always run in the container, regardless if the command flag is included or not.

The entrypoint can be overwrittten at run time with the option (using sh as an example here):

--entrypoint /bin/sh

To inspect an image:

docker image inspect <image> 

Apptainer

Linux host have apptainer (formally singularity), that can be run similarly to docker. It uses a cache directory to store the images so I suggest to set that cache to a location with large disk capacity. In the following example /path/to/user/cache is used:

export sif_cache=/path/to/$USER/sif

and then:

export APPTAINER_CACHEDIR=$sif_cache/apptainer-cache 
export APPTAINER_TMPDIR=$sif_cache/apptainer-tmp 
export TMPDIR=$sif_cache/apptainer-tmp 

apptainer exec --cleanenv --bind ~/mywork:/usr/local/mywork \
  <image> command