Hello,
When I install from binary files the boost problem doesn't go away and I get one extra error message in the beginning.
Error running cuffdiff. cuffdiff: /usr/lib64/libz.so.1: no version information available (required by cuffdiff) [14:51:54] Loading reference annotation. Warning: No conditions are replicated, switching to 'blind' dispersion method [14:52:05] Inspecting maps and determining fragment length distributions. terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injectorboost::thread_resource_error
'
what(): boost::thread_resource_error
When I inspect the file libz.so.1 I get a symbolic link to another file, libz.so.1.2.3 which appears in the same directory.
[@]# file /usr/lib/libz.so.1 /usr/lib/libz.so.1: symbolic link to `libz.so.1.2.3' [@]# file /usr/lib/libz.so.1.2.3 /usr/lib/libz.so.1.2.3: ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), stripped
-Rob
On Mon, Jun 24, 2013 at 8:15 PM, Jeremy Goecks jeremy.goecks@emory.eduwrote:
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_injectorboost::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.