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Update setup script

Kevin Pedro requested to merge github/fork/kpedro88/update_setup into Run2_2017

See commit messages for list of changes.

Still to come: mxnet files are being synced to the LPC CVMFS area. Once that is finished, the setup script can be update to install the tool directly from CVMFS (avoiding the need to carry around a 45MB library in every Condor job).

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