Error running cuffdiff. [12:48:21] Loading reference annotation.
Warning: No conditions are replicated, switching to 'blind' dispersion method
[12:48:33] Inspecting maps and determining fragment length distributions.
terminate called after throwing an instance of
'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::thread_resource_error>
>'
  what():  boost::thread_resource_error: Resource temporarily unavailable

This is a linkage error with the Boost library; you might need to modify the Boost path and then recompile Cufflinks. That said, I don't recommend compiling from source unless needed; the Cufflinks suite is provided precompiled for many platforms.

Getting the Cufflinks suite working and getting it working with Galaxy are two different things. I recommend:

(a) getting Cufflinks working from the command line first using the tutorial:

(b) doing the tutorial in Galaxy;

(c) using your own data with Cufflinks in Galaxy.

Cufflinks can run very slow, especially if using a limited number of threads, so long running time is not necessarily an indication of error.

Good luck,

J.