Hi all - I'm running Cufflinks 0.9.3 locally in my galaxy instance but it keeps failing because of information cufflinks writes to stderr. cufflinks provides the parameter "-q" to suppress this output. This needs to be included in the cufflinks_wrapper.py file.

I've made the following change at about line 90:

# Base. cmd = "cufflinks" + + cmd += " -q" + # Add options.

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Ryan,

Cufflinks' logging output should not be causing the failures that you're seeing. The Cufflinks wrapper captures the stderr messages and, if it finds an error, outputs the stderr for debugging purposes. In rare cases the logging output can cause issues; because of this, we made the change you noted a couple weeks back. This change is available in galaxy-central and will soon be available in galaxy-dist.

Best, J.

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