Update setup.md for the HPC use case

[ocaisa]

• Update the required data files (or do we only generate them instead?)
• Decide on approach(es) to make the required software for the tutorial available (snakemake, amdahl and also probably a plotting tool). Possibilities include
  • environment modules
  • pip
  • conda/mamba

[tkphd]

I think the required files are the amdahl package (if not already installed) and the plotting script. Both are Python black-box programs.

[tkphd]

Data files will be generated by Amdahl using the new terse flag.

[ocaisa]

Having to pull the tarball is a useful callback to HPC intro, and we'll still need it to pull down the plotting script (and whatever else) so we don't lose anything by generating the raw data ourselves.