Editing CommunityData:Klone (section)

== About Containers ==

We use [https://apptainer.org/docs/user/latest/index.html Apptainer] (formerly known as, and sometimes still referred to as Singularity) containers to install software on klone.  Klone provides a very minimal operating system so without these containers, installing software can be quite labor-intensive.
Our goal has been to make using software installed through apptainer as seamless as possible.  For the most part, once you have your environment configured as above, you shouldn't have to think about the containers unless you need to install something new. 

We created commands (e.g., <code>python3</code>, <code>Rscript</code>, <code>jupyter-console</code>) that run the containerized version of the program.  The full list of such commands is in <code>/gscratch/comdata/containers/bin</code>. 

Importantly, installing packages in R, Python (e.g., using pip) or other programming languages should usually work normally because the containers already have the most common dependencies.  Installing packages this way will not update the container. Instead the packages will be installed in your user directory.  This is desirable so that different container users do not break each other's environments. It may happen that an installation fails because it requires a missing dependency from the operating system.  If this happens you can try to add the dependency to the container as described below.  If this seems
challenging or complicated or you need many changes to the container, or changes you don't understand, reach out to the IT team. 

We will use multiple different apptainter containers for different applications to avoid incidentally breaking existing versions of packages during upgrades.  We want containers that include "soft dependencies" that R or Python libraries might want.