Thank you Greg, That what I tried to do initially but I could not find this tool the tool shed repository. Here is what I did, as an admin I went to Search and browse shed tool->Galaxy main tool shed Then I searched for "ngsrich" I could not find it. Then I looked under static category I still could not find it. I even went to the search page I looked for the software and still will not show up. I finally downloaded it manually but had not gone that far. I am not sure if what I did make sense or not or the right way to do. Can you please tell me how to find that tool other than what I did above? Or if what I did is missing something? I appreciate your help... From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: Thursday, February 14, 2013 5:29 PM To: Hakeem Almabrazi Cc: Galaxy Dev Subject: Re: [galaxy-dev] Install NGSRich in local galaxy Hello Hakeem, Here is a link to the tool shed wiki sections that provide all of the details for installing repositories from the tool shed into your local Galaxy instance. http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_unin... We advise that you use the automatic installation process when installing into your Galaxy instance and not the manual installation process. Greg Von Kuster On Feb 14, 2013, at 5:48 PM, Hakeem Almabrazi wrote: HI, Does anyone know who to install NGSRich software on a local instance of Galaxy? I tried to install it from the shed_tool but it does not show up in the repository, so I manually downloaded it from http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&operation=view_or_manage_repository&page=1&async=false&show_item_checkboxes=false&f-free-text-search=ngs&id=feaea37bb0f3bdca But now, I am not sure how to add it into my galaxy env. Any help will be highly appreciated ... Regards, ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/