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
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.
Texas A&M University