2.5 years ago by
You could just install a reference genome (that was GATK-sorted, see their web site and manual about how to do). This would provide a reference genome but none of the extra files.
Or you can obtain all of the data from the binary package from the GATK source and install it line-command. The same is true for certain other tool suites with reference data that is more complex than just a genome.
The Data Manager you point out is just one part of setting up the data. We welcome Data Manager contributions to the Tool Shed.
More about organizing data is in the Galaxy wiki here, including the location of our rsync server. That server is a good way to see how data is put together for http://usegalaxy.org.
Using a Custom reference genome is also a choice, please see:
Best, Jen, Galaxy team