Thanks to the help of galaxy-dev, I've been able to migrate into a MySQL backend for my local galaxy instance. My next goal is to add the datasets for different genomes (bacterial, fungal, etc), so I've decided to start with human. I started out following the wiki Data Integration page and downloaded the BigZip files (full data set) for hg19. Next, the guide mentions to check individual tool xml's to see which .location file it uses, which in turn can be used to get the file type and format needed for the file.

My first question: Is this the best way to go about adding a genome to a local instance -- Are the database files just referenced by the tools that use them, or is it possible to somehow include them in the MySQL database. Ideally I'd like to be able to select MyGenome from within Galaxy (probably through 'get Data' in the table browser ).

The problem I'm having is that I cannot find all of the required files for a lot of the tools that came with the galaxy installation. Are a lot of these files just the resulting output of a script or program? e.g. ENCODE data, sequence alignments, genomic DNA extraction, etc.