Containerized software

Containers have become a popular way to deliver bioinformatics application. It is a well-suited item to use on our server as it provides the application in a ready to go manner.

Find and download containers

You can find and download containers from the following repositories, * https://hub.docker.com/u/biocontainers * https://quay.io/organization/biocontainers

To download a container use

apptainer pull /tools/containers docker://<path to image>

This way, other can use the container too. Please inform the admins if you think others can benefit too.

Containers are piece It is possible to use containerized software through apptainer

Running containers

Apptainer automatically mounts $HOME, /tmp, and the current working directory. Extra directories are linked using bind mounts.

module load apptainer/1.5.2
apptainer exec -B /work/<user>/data:/data <my_container.sif> <command_name> --input /data

When running Apptainer, host environment variables pass through into the container unless isolated. To control runtime behavior cleanly, use these mechanisms:

apptainer exec --cleanenv my_container.sif python script.py

or use a wrapper script:

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#!/usr/bin/env bash
apptainer exec --cleanenv /path/to/software.sif software_bin "$@"

Conda environments

We discourage the use of conda environments, but recognize they are sometimes needed. If you want to create a conda environment, please follow these rules:

• to use conda, use the available module (module load miniforge/26.1.1)
• environments need to be created in /tools/sw/container/miniforge/26.1.1/envs to ensure availability on all compute nodes in case of questions, as the administrators