Clarify software requirements

[mfansler]

The Python software requirements are listing modules that are loaded, including some system modules that shouldn't need specification.

### python package dependency
- sys (*core*)
- gzip (*core*)
- pysam
- click
- os (*core*)
- pickle (*core*)
- numpy
- pandas
- progress.bar (**<- unclear**)
- collections (*core*)

It would be better to provide a Conda YAML or lockfile to define the software packages that need to be installed, rather than the module names. It is not always the case that module names correspond to package names (PyPI or otherwise).