Cuffdiff 2.2.1.5 SQLite option results in job failures

This is the most current version on the tool shed and it always fails when the SQLite option is used.

History of the problem as it presented at https://usegalaxy.org: https://github.com/galaxyproject/usegalaxy-playbook/issues/50

What we are telling users to workaround the problem (for at least the last 4 months): https://biostar.usegalaxy.org/p/26894/#27025. In short, to use the earlier version: 2.2.1.3.

Merged duplicated Biostars posts into this one, use as the master for reported problems and final resolution: https://biostar.usegalaxy.org/p/26894/

ping @natefoo @martenson @davebx