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glossaries texstudio and miktex portable

I am not quite sure if this question is on the right sx site but since it is heavily tex related I figured I ask here.

My setup consists of a windows machine with texstudio and miktex, both in the portable version. I am trying to use the glossaries package.

To do so I want to run makeglossaries by means of a custom user command. However when I try this it complains about not finding makeindex on the path. However i added miktex's bin folder to the user-path variable and if i type makeindex from a commandprompt outside miktexs bin folder it works just fine.

What is the proper way of using makeglossaries(.bat) with the portable miktex/texstudio setup?

Edit: I expiremented with changing the command line. If I supply the -d option to makeglossaries, which sets the path in which to run makeindex, i can get it to find makeindex, however, this causes several further issues: I need to supply absolute paths for the index style with -s, and absolute paths to the temporary files, which then can't be written due to miktexs security feature.