Add a line to ~/.bashrc that points to your .cls files
The . in front is critical to source the current directory
For example, my github (http://www.github.com/kastnerkyle/Papers/) has an IEEEtran file that has the IEEE standard template inside. To use it, simply add this line to ~/.bashrc
export TEXINPUTS=.:<path_to_IEEEtran_file>:$TEXINPUTS
now running texi2pdf should compile IEEE format .tex files
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