Cluster installation

It is likely that you will eventually want to run CYTools on a cluster. The problem is that clusters generally don't allow you to use Docker, as it requires admin privileges. For this reason, we made this guide to help you set up CYTools using a Singularity container. Singularity is a containerization tool similar to Docker. It only works on Linux and is a bit more tricky to set up, but it allows for more flexible usage that doesn't require admin privileges. Most likely the cluster of your choice will have Singularity available to use.

info

At some point we want to offer a self-contained script that installs CYTools and all of its dependencies without any admin privileges. However, this is a tricky task and we haven't been able to fully do it. If you would like to help us please let us know by emailing us at [email protected].

Installation instructions​

The simplest way to build a CYTools Singularity image is with the pre-built Docker image that we host on Docker hub.

1. All you have to do is make sure that your cluster has Singularity installed, and run the command.
singularity build cytools.sif docker://liammcallistergroup/cytools:singularity

And that's it! You will end up with a cytools.sif file that contains all of CYTools.

Usage​

The full documentation on how to use Singularity containers can be found at this link. For example, if you want to start a Python shell to do some computations with CYTools you can run

singularity exec cytools.sif python3

Since the CYTools is primarily tested with Docker it is possible that some functionality doesn't work properly with Singularity. If this is the case, please let us know by emailing us at [email protected].