Re: [galaxy-dev] cufflinks libz error/warning

2011-03-18 Thread Ryan Golhar



On 3/17/11 10:01 PM, Jeremy Goecks wrote:

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.





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...
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Re: [galaxy-dev] cufflinks libz error/warning

2011-03-18 Thread Jeremy Goecks



 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.
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[galaxy-dev] cufflinks libz error/warning

2011-03-17 Thread Ryan Golhar
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?


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Re: [galaxy-dev] cufflinks libz error/warning

2011-03-17 Thread Jeremy Goecks
 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.
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