Change pip install strategy

[kopardev]

https://github.com/CCBR/CHAMPAGNE/blob/2392eab521ce75dd818ddd74eb733a3ad5ffe6c8/README.md?plain=1#L26

This will install the champagne executable in pip's default location. We may want to change this with something like this:

% pip3 install --target=`pwd` .

or something to have different self-contained champagne executables in case you have multiple concurrent instances/versions of CHAMPAGNE. PYTHONPATH may also need an update accordingly.

Another issue here is we are assuming that pip3 is in PATH. When installing on biowulf/frce, we may have to:

• source conda
• activate conda environment with pip3 etc.
• run pip3 install

Also, does this mean that the same conda environment is required when you actually run champagne??... Something to think about.

Again, our user base does not need to know how to install champagne ... this could go in "docs" about how to install on HPC other than biowulf/frce. ... but if on biowulf then simply do module load ccbrpipeliner and voila!

[kelly-sovacool]

We'll bury this in the docs for devs, as biowulf and frce users will have it installed in the module and aws users can do nextflow run CCBR/CHAMPAGNE.