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Ive added a setup.py, allowing phylowgs to be installed into site-packages and used on the commandline. phylowgs_evolve, phylowgs_write_results, phylowgs_create_inputs and phylowgs_parse_cnvs are now on the command line after running setup.py. Note that some files had to be moved. Also, evolve expects phylowgs_mh (not mh) to be on the path. The easiest is to install using conda (recipe included in pull request),

cd conda
conda build phylowgs

Then your users can

conda install phylowgs

And use phylowgs_evolve without any other setup. To get that to work you have to change the git_rev in meta.yaml to a git revision after this pull request, conda build phylowgs on a general linux, and upload to anaconda.org using the command it spits out at the end of the build.

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