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-mnt

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-to-Cloudman-by-FTP-td4661119.html) 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