Here's the usage:
./autoscript /path/to/samples /path/to/refpanel snp.set
There are samples already in the samples/ folder or you could play with a few from www.opensnp.org
As for reference panel, unzip PHYLO.zip from this github repository by Razib Khan and place those files in reference_panel/. ( If you want super continental ancestry, use the PHYLO.fam already in place. )
I have provided a SNP set of ~9000 SNPs which gives accurate ancestries for large samples so far. The SNP set will be expanded to ~20000 soon.
./autoscript samples reference_panel/PHYLO ancestry.snps
Use the PHYLO.fam in place for super population ancestry calculation. I have presented the way I mapped a subpopulation to a super population in the pops2region.txt file.
After the script is done running on a file in samples/ it will produce an ancestry png file which you could choose to save. Press enter after viewing the file for it to run on the next file in the folder.