What is Container Image?

…in a nutshell

A Container Image is an image file with packaged code (software applications) along with its dependencies (e.g., specific operating system, system libraries) that can be deployed consistently as a container in any environment.

Since the image is unchangeable after it is built, it allows for consistent and repeatable deployment. For example, let’s say an image was built with Ubuntu as the operating system, and you deploy this image on your Windows 11 PC (host). A Ubuntu “container” will be created and the programs inside this container will run under the Ubuntu settings.

Different platforms are available for building and deploying these container images, for example, Apptainer, SingularityCE or Docker.

For the MIMA Pipeline we use Apptainer.

Noteworthy points

Build a Sandbox

Every time you deploy a container from an image file (*.sif extension), the platform needs to unpack the system files each time. If the container is complex and have many dependencies or programs, this can be time consuming.

You can bypass this by building a sandbox that unpacks the files once into a directory (container in a directory) and then repeatedly use that directory. This removes the need to keep unpacking each time.

apptainer build --sandbox <container-directory> <image.sif>

Containers need explicit instructions to access your files

A container is deployed with the bare minimum filesystem to operate, meaning that it only has access to your home directory by default.

It does not automatically have access to other filesystems or disks. If your data is located on another drive or path, then you need to explicitly provide this information using either

Option 1) -B parameter: the binding only exists during the life of the container

apptainer run -B /home/jsmith/studyABC:/study/data,/srv/shared/refDB:/reference/data

Option 2) APPTAINER_BIND environmental variable: the binding exists during your terminal session (multiple deployed containers)

export APPTAINER_BIND="/home/jsmith/studyABC:/study/data,/srv/shared/refDB:/reference/data"

The path binding format is: <host-PC>:<container> where the:

• Left of the colon (:) is the absolute path of the directory found on the host PC
• Right of the colon (:) is the path that the Container sees when it’s deployed

The above example: