First rollout version of eukrhythmic

This first rollout of the pipeline includes several user configuration options, including:

• User editing of configuration YAML file (config.yaml)
• Command-line arguments for aliased executable file
• Script for submitting to scheduling platform using command-line arguments

The features of the pipeline have been more inclusively updated in the documentation, and user customization is supported for the existing assemblers (including the sample run setup), as well as for adding other assemblers.