You could obtain the version of this genome from the GATK source bundle and use it as a custom reference genome.
I should let you know that using such a large custom genome with GATK tools at http://usegalaxy.org will likely create jobs that are too large to complete.
Also, the GATK version at this public site is older and the wrapper deprecated - meaning, they may not include all of the best practice tools you wish to use, may fail for odd reasons that will not be fixed, and the like.
The other option is to start up a local or cloud Galaxy, install the tools, install the reference genome, create indexes, and proceed.
- Fasta Format, Custom Genomes, and GATK Chromosome ordering
Thanks, Jen, Galaxy team