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.
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, 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. ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
participants (2)
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Goecks, Jeremy -
Ryan Golhar