> 
> 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:

http://cufflinks.cbcb.umd.edu/tutorial.html

(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.
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