Full Pipeline, QC, & Phasing Update

Built out the Graphical User Interface and established each part of the pipeline as a button to be run individually or as a whole pipeline. Also updated the setup shell script to aid in ensuring there is an environments available with all necessary requirements. This update does use the Phased Haplotype .fasta file in MycoMap summarizing, it can however, still use the default features developed by Stephen Douglas Russell. A Quality Control feature: Nanofilt via Chopper is implemented to ensure reads going through the pipeline are of specific quality and length. The main menu has also been updated to include space for variable command options for Chopper, Minibar, and NGSpeciesID.