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.


Ryan

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