Hi Jeremy Thank you so much for your help I will be trying these solutions Here the picture, I hope can you can view it [cid:image001.jpg@01CDC80C.84421B20] Best regards, Mira From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] Sent: Wednesday, November 21, 2012 5:10 PM To: Dr. Mira A. Bisso Cc: galaxy-dev@lists.bx.psu.edu Galaxy-dev Subject: Re: [galaxy-user] help Because your questions are about a local installation of Galaxy, your email is best suited to the galaxy-dev mailing list, so I've moved it there. 1. FastQC not running . gives an error and doesn't run on groomed or un-groomed FastQ file. The error message shows in the below pic. I don't see the pic, you probably need to install FastQC: (a) download the tool (b) put the fastqc script in the <galaxy_home>/tool-data/shared/jars/FastQC directory (c) make the script executable: %chmod 777 <galaxy_home>/tool-data/shared/jars/FastQC/fastqc 2. No reference genomein the drop down list in TOPHAT for illumine tool and TOPHAt2. See the section 'Setting Up the Reference Genomes for NGS Tools' on this page for help setting up genomes/indices: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Best, J.