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 -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.