I have added the makeglossaries script to the list of scripts available in miktex. It's working fine, but the problem is that it first requires pdflatex to run. Also makeIndex and bibtex should be run afterwards. So the final order of scripts that need to be runned look like this:
pdfLatex -> MakeGlossaries -> pdfLatex -> MakeIndex -> bibtex.
At the moment i'm executing the scripts in this order manually but i was wondering if there is also a way to let miktex combine them in the right order and execute them after each other automatically?