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The hardcoded variables in run_e2e_ver.sh and run_pyrosetta_ver.sh make it not conducive to installing this software centrally on an HPC cluster, as it requires write permission for someone to change the CPU and MEM values should they want to.
These changes implement a print_usage -h|--help function and getopt to allow a user to dynamically set those values, along with command line options for the path to their input fasta (the only required option), working directory, and path to database files.