I created a local instance of Galaxy (Ubuntu OS) and It came with only a very few tools compared to public instance. e.g. all NGS: QC and Manipulation, NGS: Mapping etc were not included. My question is: Did I make a mistake in creating the local instance ? Or do I have to integrate them manually ? Is there any other efficient way to do it.
everything is fine :) You should read our documentation about setting up a Galaxy instance which you can find here: https://wiki.galaxyproject.org/Admin. Especially interesting for you is probably this sub-page: https://wiki.galaxyproject.org/Admin/Tools