Containers
Containers
Containers are a way of sharing software across different systems. On the Tufts HPC Cluster we can use the Singularity module (now called Apptainer) to build containers on the cluster.
Building An Outside Container On The Cluster
- To begin you will need to load the following modules:
module load singularity/3.6.1
module load squashfs
- Now, search docker hub for the tool of your choice. You will be using this image to build a singularity container or sif file. In this case we will be demonstrating how to download the biobakery workflows docker image:
singularity build bioBakery.sif docker://biobakery/workflows
Using The Container
- To use this tool you will need to reference the sif file you created. So to run the humann3 command you would use the following:
singularity exec bioBakery.sif humann3 --help