Merge pull request #8 from johnb30/master

Update README
Extensive changes to handle uploads, file names from PHOX_config.ini, and standardize error handling
Delete default.config.ini (PHOX_config.ini replaces)
Merge pull request #9 from philip-schrodt/master

Extensive pipeline changes
Added example of PHOX_config.ini to README.md
Merge pull request #15 from philip-schrodt/master

Added example of PHOX_config.ini to README.md