Sort out exact dependencies

[fedarko]

See https://github.com/fedarko/sheepgut/blob/main/environment.yml.

A few conda things (minimap2, samtools, CheckM, prodigal) will likely need to be installed first. Figure out what the easiest way to set things up will be; maybe it'll be faster to get this up on Conda than PyPI.

Makes sense to document dependencies on a module-by-module basis:

• strainflye align
  • minimap2
  • samtools
  • networkx (needed for loading GFA during partially-mapped-reads filtering)
  • pysam
  • scikit-bio

[fedarko]

I think for now we can just ask users to install the conda prereqs, then install the actual package via pip. If we can get this on conda easily then it'll just be one step, but that's another can of worms