The makeindex and xindy. MakeGlossariesGUI will attempt to locate them on your system's path, but if they can't be detected, you'll need to specify the correct location. You can omit the location for an unrequired application.tab lists the paths to
MakeGlossariesGUI will try to determine the language and input encoding from the .aux file to pass to xindy, but you can override this if you want to. Make sure that the check box is selected, and change the language and encoding as appropriate. Note that the batch mode will also use these settings, although they can only be adjusted in the GUI mode.