Hello Luciano,
The problem is resolved by using the chmod command below.
Thanks a lot.

From: Luciano Cosme [mailto:cosme.sim...@gmail.com]
Sent: Friday, July 06, 2012 9:58 PM
To: Aarti Desai
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Permission denied error when running fastqc

   You will have to change the permission of fastqc to be executable. You can 
open your terminal, log as root and change it. Open your terminal, type sudo 
su, then it will ask your password. After you enter your password type chmod 
777 /root/Programs/Galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc


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