Containers

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 other computer and then transfer the container to the wharf.

• Gatk is developed by Broad institute

Can I find it on sylabs.io?

• https://cloud.sylabs.io/
• Search for gatk

Well. It is there but broadinstitute is not there. Let's look for alternatives, otherwise we get back here!

• Continue to Dockerhub.

• https://hub.docker.com

• Search for gatk

• Several ones show up. the latest (and official "Broad institute" one) would be the best!
• https://hub.docker.com/r/broadinstitute/gatk/

Perfect!

• Log in to transit: ssh <username>@transit.uppmax.uu.se
  • Documentation
• (If not done already) Mount the wharf of your project.

user@transit:~$ mount_wharf sens2025560
Mounting wharf (accessible for you only) to /home/<user>/sens2025560
<user>-sens2025560@bianca-sftp.uppmax.uu.se's password:

• Navigate to your wharf folder

cd sens2023531

• Disable Singularity cache

export APPTAINER_DISABLE_CACHE=true
export APPTAINER_TMPDIR=/dev/shm/$USER
mkdir -p $APPTAINER_TMPDIR
unset ${!NXF_*}

• You can get the container here directly with the "pull" command
• Run the command:

apptainer pull gatk_4.6.2.0.sif docker://broadinstitute/gatk:4.6.2.0

• In a Bianca session, navigate to the wharf

cd /proj/sens2025560/nobackup/wharf/$USER/$USER-sens2025560

• Move it to the project folder (good practice)

mv gatk_4.6.2.0.sif /proj/sens2025560/$USER/

• Go there

cd /proj/sens2025560/$USER/

• Run it:

`apptainer exec gatk_4.6.2.0.sif gatk`

It should give some output but it may give some warnings

Set the Apptainer cache directories to /proj/<proj-id> to prevent quota issues

mkdir -p /proj/sens2025560/$USER/apptainer_cache_dir/{cache,tmp,localcache}
export APPTAINER_CACHEDIR=/proj/sens2025560/$USER/apptainer_cache_dir/cache
export APPTAINER_TMPDIR=/proj/sens2025560/$USER/apptainer_cache_dir/tmp
export APPTAINER_LOCALCACHEDIR=/proj/sens2025560/$USER/apptainer_cache_dir/localcache

More info

Singularity course