Previously, we created a conda environment with a specific name and then manually added this directory to the PATH. This worked fine, but felt a little hacky. After some discussion (@apeltzer @sven1103 @ewels @pditommaso and others), we removed it. Instead, we now install the environment to the base conda environment.

This all seemed fine, until we just came across a strange bug. After some investigation, it seems that the host filesystem conda installation was taking priority over the base conda environment (due to configuration files in the home directory). Combined with conflicting path mounts we ended up with a steaming mess and non-functional software. This issue creates two problems:

• Software breaks (as above)
• Software works, but is actually the host installation and not from the container (not reproducible)

Either we need a fix, or we can revert to the previous method. Manually prepending to the PATH env skips all of these problems, as we're essentially not using conda any more.