I originally planned to run GREAT locally from the start but ran into issues with compiling. Instead, the current implementation uses the rGREAT package, which sends requests to the GREAT server. This works well but is slow since calls are limited to one request every 5 minutes. The 215 zebrafish miRNAs therefore took over 18 hours to run. TargetScanHuman contains nearly 10,000 miRNAs (~35 days to run!!!), so it would be much better to run GREAT locally and cut this down to ~1min/miRNA.
Since I had problems with macOS, it would probably be best to attempt this in a linux environment.
I originally planned to run GREAT locally from the start but ran into issues with compiling. Instead, the current implementation uses the rGREAT package, which sends requests to the GREAT server. This works well but is slow since calls are limited to one request every 5 minutes. The 215 zebrafish miRNAs therefore took over 18 hours to run. TargetScanHuman contains nearly 10,000 miRNAs (~35 days to run!!!), so it would be much better to run GREAT locally and cut this down to ~1min/miRNA.
Since I had problems with macOS, it would probably be best to attempt this in a linux environment.