the tool you ask about seems to be a shell script that runs additional software like plink and beagle

both of these tools can be easily installed in a linux-like system using a tool like conda or micromamba

now snp2hla program seems fairly old, from 2016, so there may be changes to how the required software operates.

I would look at what the snp2hla program does, notably the file:

SNP2HLA/SNP2HLA.csh 

then running those steps separately and figuring out what takes place.

• Plink: https://zzz.bwh.harvard.edu/plink/
• Beagle: http://faculty.washington.edu/browning/beagle/beagle.html