Thank you for the reply.
I do not have any working knowledge of ubuntu and linux commands.
Moreover, I work from a windows computer.
I can see that this problem is being discussed since July12th 
http://dev.list.galaxyproject.org/Cloudman-Software-does-not-work-due-to-broken-symlinks-td4660619.html
When will this bug be solved?
I terminated my cloudman instance with frustration.

Anto

Anto Rajkumar, MD, DNB, MRCPsych,
PhD fellow, Department of Biomedicine,
Aarhus university,
8000 C, Aarhus, Denmark.
E-mail: APR@hum-gen.au.dk
From: Ravpreet Setia [Ravpreet.Setia@oicr.on.ca]
Sent: 13 August 2013 17:02
To: Anto Praveen Rajkumar Rajamani; clements@galaxyproject.org
Cc: galaxy-dev@bx.psu.edu
Subject: RE: [galaxy-dev] Cloudman could not determine the version of Tophat and cufflinks.

I think you are experiencing this bug, which is a major problem with the latest AMI. 



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