What are your goal(s)?
- Install reference genomes into your own Galaxy server?
- Learn the source of a particular reference genome available at a public server?
- Exact sequence data from a reference genome (based on coordinates) that is already indexed on a server you are working on or some custom reference genome fasta you have in your history?
- Other?
Running Data Managers to install genomes is an administrative function, and these can be run with web-based tools or line-command. You would need to be the administrator of the server to install a new built-in genome. The exact genomes installed at usegalaxy.org (and mostly also usegalaxy.eu) are available here: http://datacache.galaxyproject.org/. However, I’m guessing that this is not your goal – am just clarifying how this works/where to find the data.
The Custom Genome/Build functions allow anyone to use a fasta uploaded into a history the same way as a native genome index is used with tools. This is web-based end-user functionality and not an administrative function. FAQ: Preparing and using a Custom Reference Genome or Build
If you just want to extract sequence data from some genome (custom fasta in your history, or indexed genome on the server), then a tool like bedtools GetFastaBed use intervals to extract sequences from a FASTA file is a good choice.
Thanks!