> ok - I managed to compile cufflinks myself.  When I run it I get a line of 
> output that reads "linked against Boost version 104601".  When I run 
> cufflinks in Galaxy, Galaxy complains about this line being an error.
> Hmmm.  How is cufflinks running in the public version of galaxy?


We compile Cufflinks ourselves as well for main, but for some reason we don't 
see the message that you're seeing when Cufflinks is run. We have Cufflinks 
v0.9.3, but I wonder whether we might be using a slightly older version of the 
code. In any case, looking at the Cufflinks code, I see:

cufflinks.cpp:85:    fprintf(stderr, "linked against Boost version %d\n", 
gtf_to_sam.cpp:46:      fprintf(stderr, "linked against Boost version %d\n", 

Try removing these lines and recompiling cufflinks; this should solve your 


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