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TeXShop allows you to add “engines” for compilation processes.
You can create a shell script and name it
<script name>.engine, make it executabel and install it under
An example for compiling a nomenclature:
#!/bin/sh style='/usr/local/texlive/2011/texmf-dist/makeindex/nomencl/nomencl.ist' bfname=$(dirname "$1")/"`basename "$1" .tex`" makeindex "$bfname".nlo -s "$style" -o "$bfname".nls
This example was adapted from an example for making a glossary found here.