The GATK tools hosted at https://usegalaxy.org are from a very old version (1.4) and have been deprecated for some time now. These are natively indexed for hg_g1k_v37 (1000 Genomes) and not hg19 (UCSC). Using hg19 from the history as a custom reference genome will cause several to fail for exceeding memory resources. We strongly recommend that you avoid using these tools.
Instead, please see the variant analysis tutorials here that include the most current tools and methods:
Thanks! Jen, Galaxy team