Start by making sure that all of the instructions at http://getgalaxy.org are followed (the first wiki, and Production server as needed). More help can be found under: https://wiki.galaxyproject.org/Admin
To install any tool, become an administrator on your instance, then use the top "Admin" tab. Under the section "Tool sheds -> Search and browse tool sheds" access the Main Tool Shed to install tools. Installed tools can be reviewed under "Server -> Manage installed tool shed repositories". To learn which exact repository is a match for a tool on an existing Galaxy instance, bring that tool up in the server's UI, and use the upper right corner pull down menu. A link to the Tool Shed will be present.
Best, Jen, Galaxy team
Hello! Did you ever get a solution? I am having the same exact problem. All of the NGS tools are available on the main galaxy page but not in the tool shed. I cannot find them in the experimental tool shed either (e.g. convert solid output to fastq).