Containers¶

Apptainer

Why?¶

Do you need a program that has a very complicated and exhausting install? Or maybe your installation requires root privileges?

Within a container you can install whatever you want and send it to whichever computer you want to run it from.

How?¶

You can either download an existing container containing your software of interest or build one yourself.

Docker vs Singularity/Apptainer¶

Docker requires root privileges and therefore are run on local computers or the cloud.

HPC-clusters without root privileges uses Apptainer.

Public repositories¶

Dockerhub is the most common and has the biggest repository: https://hub.docker.com/

Apptainer/Singularity uses: https://cloud.sylabs.io/library Luckily, Apptainer can convert docker containers into Apptainer containers.

Anyone can upload a container to the repositories. So be cautious and look for verified publishers.

Learn more about containers¶

Read more on the Uppmax singularity workshop: https://pmitev.github.io/UPPMAX-Singularity-workshop/

Example: I want gatk on Bianca¶

Remember, no internet on Bianca. Build on Rackham and then transfer the container to the wharf.

Can I find it on sylabs.io?

https://cloud.sylabs.io/library/search?q=gatk

No.

Continue to Dockerhub.

Dockerhub?

- <https://hub.docker.com/r/broadinstitute/gatk/>

Perfect.

Note that apptainer is not a module but available like a system tool! apptainer pull gatk_4.3.0.0.sif docker://broadinstitute/gatk:4.3.0.0

apptainer_pull

sftp to the wharf:

sftp_gatk

apptainer exec gatk_4.3.0.0.sif gatk

apptainer_gatk

Set the Apptainer cache dirs to /proj/proj-id to prevent quota issues¶

mkdir -p /proj/staff/bjornv/apptainer_cache_dir/{cache,tmp,localcache}
export APPTAINER_CACHEDIR=/proj/staff/bjornv/apptainer_cache_dir/cache
export APPTAINER_TMPDIR=/proj/staff/bjornv/apptainer_cache_dir/tmp
export APPTAINER_LOCALCACHEDIR=/proj/staff/bjornv/apptainer_cache_dir/localcache

More info

Singularity course