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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.

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I have no TeXStudio and MiKTeX in portable version so I can't check it, but

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I think this would have been better as a comment. Now to the questions you reference: 1) I do not want to use a custom index style file, since glossaries comes as a package and everything else is found besides the sty file to format the finished glossary I do not see how a custom tree helps if most parts of the package are found (including makeglossaries). 2) I managed to confiugre all other tools with relative paths, also it finds makeglossaries, but makeglossaries does not find makeindex in turn 3) see 2), I can manage with the relative paths "../Miktex/miktex/bin/makeglossaries.exe" – ted Aug 9 '13 at 17:59
I do not mean to be offensive but the path to makeglossaries works, however makeglossaries fails to find makeindex if called from tex studio. I appreciate your effort, but I think in case of a link collection which can be partly found in the Related bar, you should use comments because if I would find my solution there it would be a duplicate/bad question. – ted Aug 9 '13 at 18:03
@ted Perhaps you can then add what you have til now? As you wrote "I need to supply absolute paths for the index style with -s" my suggestion seems to be a possibility I can not test because I have no portable system here. – Kurt Aug 9 '13 at 18:12
I got Texstudio to run makeglossaries from the menu. However makeglossaries complained that it could not find makeindex, eventhough I put it on the PATH thus I supplied the path to makeindex to makeglossaries with the -d option, which in turn gave the error that the style file was not found, so I supplied the path to the stylefile with the -s option which lead to a nother error that the file could not be written. I put a link explaining the last issue in the question and explained all this in the question. currently i run makeglossaries from the shell. – ted Aug 9 '13 at 18:18

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