I have reinstalled cufflinks from source and now I get a new error. I am using the Cuffdiff wrapper (version 0.0.6) and cufflinks-2.1.1. The boxes come back green but there is no output and there is a message in the standard error box.

Error running cuffdiff. [21:34:00] Loading reference annotation.
Warning: No conditions are replicated, switching to 'blind' dispersion method
[21:34:12] 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

WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'blastxml': 'module' object has no attribute 'BlastXml'
WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'wsf': 'module' object has no attribute 'wsf'
WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.xml:BlastXml' to sniff_order: 'module' object has no attribute 'BlastXml'

Thankyou,

-Rob

On Tue, Jun 11, 2013 at 5:40 PM, James Taylor <james@jamestaylor.org> wrote:

> [galaxy@q ~]$ /bin/cuffdiff
> /bin/cuffdiff: /usr/lib64/libz.so.1: no version information available
> (required by /bin/cuffdiff)
> cuffdiff v2.0.2 (3522)

This definitely indicates a problem with your cuffdiff install. Did
you build cuffdiff on that system or install in some other way? (very
odd to have it installed in /bin).