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?