stevemussmann/admixturePipeline: AdmixPipe v3.0

v3.0 has several "behind the scenes" changes, bug fixes, and enhancements to existing modules. Two new modules have also been developed for the following purposes:

1. automatic submission of admixturePipeline.py output to the CLUMPAK website.
2. assessment of the best K using the evalAdmix package (http://www.popgen.dk/software/index.php/EvalAdmix).

Other important notes for v3.0:

1. Some outputs from AdmixPipe v2.0 are incompatible with v3.0 because I now use json files to track data and file names from early parts of the pipeline that are needed in some of the later modules.
2. Whereas AdmixPipe v2.0 was backward compatible with Python 2.7.x, v3.0+ requires Python 3.
3. Some command line options have changed slightly (especially long form commands - you can get the current list of commands by running any module with the --help option).
4. There is now a Docker container to streamline the installation process.
5. The submitClumpak.py module is completely optional. You can accomplish the same results by manually submitting your admixturePipeline.py module outputs to the CLUMPAK website.
6. The submitClumpak.py module will not function in the Docker container. If you wish to use it, this module must be set up on your own computer. It requires selenium and currently is only compatible if you have Firefox installed.
7. The data processing and plotting functions of the cvSum.py module underwent a complete rewrite for v3.0.