Thanks for clarifying, @bennet, that sounds exactly like what we have implemented. It sounds like you are in the same boat where you need to module load Bioinformatics before you can load samtools for instance.
From the OOD point of view, does module load Bioinformatics samtools work, or do you have to load Bioinformatics module before you try to load samtools. The issue I had, is that in our environment, I had to load chemistry gateway module which presumably injected the “space” into MODULEPATH before I could load cdd/prd modulefile.
This is why I converted the module load to a loop in the script.sh.erb template. I am waving my hands a little bit here because I wasn’t the guy that implemented the Lmod app spaces/gateway modules :D.