I think you are experiencing this bug, which is a major problem with the latest AMI. https://bitbucket.org/galaxy/cloudman/issue/6/tool-default-symbolic-links-to... ________________________________ From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of Anto Praveen Rajkumar Rajamani [APR@hum-gen.au.dk] Sent: Tuesday, August 13, 2013 4:05 AM To: clements@galaxyproject.org Cc: galaxy-dev@bx.psu.edu Subject: [galaxy-dev] Cloudman could not determine the version of Tophat and cufflinks. Hello, Along with the Tophat (could not determine version: http://dev.list.galaxyproject.org/Problems-with-Tophat-amp-uploading-files-t...) problem in my cloudman, I experience a similar problem with Cufflinks. I uploaded a trial BAM file and ran cufflinks 0.0.6. The run failed and I got a message that "Could not determine the version of Cufflinks". When I tried to report the bug using the green bug icon, I get a message "Mail is not configured to report this bug". I updated my Galaxy to http://bit.ly/galaxy20130812 and restarted my instance. My instance is on, but I am unable to analyse my data. Where do I go wrong? Kindly help me to solve this problem. Thank you. Best wishes, Anto