Hello,<div><br></div><div>When I install from binary files the boost problem doesn&#39;t go away and I get one extra error message in the beginning.</div><div><br></div><div><pre style="word-wrap:break-word;white-space:pre-wrap">
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 &#39;blind&#39; dispersion method
[14:52:05] Inspecting maps and determining fragment length distributions.
terminate called after throwing an instance of &#39;boost::exception_detail::clone_impl&lt;boost::exception_detail::error_info_injector&lt;boost::thread_resource_error&gt; &gt;&#39;
  what():  boost::thread_resource_error</pre></div><div>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. </div><div><br></div><div><div>[@]# file /usr/lib/libz.so.1</div>
<div>/usr/lib/libz.so.1: symbolic link to `libz.so.1.2.3&#39;</div><div>[@]# file /usr/lib/libz.so.1.2.3</div><div>/usr/lib/libz.so.1.2.3: ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), stripped</div></div><div>
<br></div><div>-Rob<br><br><div class="gmail_quote">On Mon, Jun 24, 2013 at 8:15 PM, Jeremy Goecks <span dir="ltr">&lt;<a href="mailto:jeremy.goecks@emory.edu" target="_blank">jeremy.goecks@emory.edu</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div><div class="im"><blockquote type="cite"><pre style="font-size:medium;white-space:pre-wrap;width:50em">
Error running cuffdiff. [12:48:21] Loading reference annotation.
Warning: No conditions are replicated, switching to &#39;blind&#39; dispersion method
[12:48:33] Inspecting maps and determining fragment length distributions.
terminate called after throwing an instance of
&#39;boost::exception_detail::clone_impl&lt;boost::exception_detail::error_info_injector&lt;boost::thread_resource_error&gt;
<span style="color:rgb(101,55,156);white-space:pre-wrap">&gt;&#39;</span>
  what():  boost::thread_resource_error: Resource temporarily unavailable
</pre></blockquote></div>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&#39;t recommend compiling from source unless needed; the Cufflinks suite is provided precompiled for many platforms.</div>
<div><br></div><div>Getting the Cufflinks suite working and getting it working with Galaxy are two different things. I recommend:</div><div><br></div><div>(a) getting Cufflinks working from the command line first using the tutorial:</div>
<div><br></div><div><a href="http://cufflinks.cbcb.umd.edu/tutorial.html" target="_blank">http://cufflinks.cbcb.umd.edu/tutorial.html</a></div><br><div>(b) doing the tutorial in Galaxy;</div><div><br></div><div>(c) using your own data with Cufflinks in Galaxy.</div>
<div><br></div><div>Cufflinks can run very slow, especially if using a limited number of threads, so long running time is not necessarily an indication of error.</div><div><br></div><div>Good luck,</div><div>J.</div></div>
</blockquote></div><br></div>