I am using a solution to an issue I am having with generating a glossary found here:
As part of the solution, Christian Hupfer suggests compiling with the following command pipeline
pdflatex foo makeindex -s foo.ist -o foo.gls foo.glo pdflatex foo
I noticed that when I am trying to compile in TeXworks using the pdfLaTeX + makeindex + bibtex command, that it fails to generate the glossary because it is missing the foo.ist, foo.gls, foo.gls files.
To solve this, I simply wrote a one line batch file:
makeindex -s workingpaper.ist -o workingpaper.gls workingpaper.glo
which I run prior to compiling my document with the aforementioned pdfLaTeX + makeindex + bibtex option.
However, looking through the TeXworks preferences under typesetting options, I get the sense that I don't need the batch file at all and I can set TeXworks to do it for me without the need to rewrite the batch file for every paper I have that I intend to include a glossary (i.e., substituting "foo" with the appropriate file name).
I've tried editing some of the existing processing tools in the preference menu to get an idea of how I might do this, but the syntax is sufficiently foreign to me that I am completely lost.
I am running MikTeX 2.9 incase this is helpful information.