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?

Jeremy,    I believe Galaxy need to update not only Cufflink 0.9.3 but  also TopHat 1.2.0.   Thanks

--- On Thu, 3/17/11, Jeremy Goecks jeremy.goecks@emory.edu wrote:

From: Jeremy Goecks jeremy.goecks@emory.edu Subject: Re: [galaxy-dev] cufflinks libz error/warning To: golharam@umdnj.edu Cc: "galaxy-dev@lists.bx.psu.edu" galaxy-dev@lists.bx.psu.edu Date: Thursday, March 17, 2011, 9:01 PM

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?

Ryan,

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", BOOST_VERSION); gtf_to_sam.cpp:46:    fprintf(stderr, "linked against Boost version %d\n", BOOST_VERSION); --

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

Thanks, J.

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...

It looks like the output only occurs when cufflinks can't run on the provided dataset. I checked my inputs, and I think that is the problem...its a sam file from bowtie, not from tophat, hence not a sorted sam file. Perhaps this stderr message doesn't matter after all, its just misleading...

Yes, I think you are correct. Let us know if you have more questions.

Best, J.