[galaxy-dev] cufflinks libz error/warning

Ryan Golhar golharam at umdnj.edu
Thu Mar 17 21:01:40 EDT 2011


On 3/17/11 3:40 PM, Jeremy Goecks wrote:
>
>     Hi all - I'm running Galaxy on my Redhat linux cluster.  When I run
>     cufflinks from the shell I get the error/warning:
>
>     cufflinks: /usr/lib64/libz.so.1: no version information available
>     (required by cufflinks)
>
>
>     but it still seems to run ok.  It looks like Galaxy is choking on
>     this.  I tried compling cufflinks manually but that was more
>     troublesome.  Is there a way I can get Galaxy to ignore this error
>     and continue?
>
>
> Ryan,
>
> There's currently no way to tell Galaxy to ignore some error messages
> and not others; we're working on this functionality but it's far from
> being done*. Unfortunately, your best bet is to compile Cufflinks on
> your system. FYI, here's a technical description of this problem:
> http://seqanswers.com/forums/showthread.php?t=8042
>
>
> *To detect particular errors, we envision XML elements in a tool's
> output definition that use regular expressions to identify errors
> amongst a program's output. We think this is the right approach, but we
> haven't started implementing it yet. You are welcome to do so; we
> welcome code contributions from the community.
>
> Thanks,
> J.

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?


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