I’m using the Extract Genomic DNA tool on usegalaxy.org. I need to choose the source for the reference genome, and if I select a locally cached, no options show up. My input database file is associated with the reference hg38 already. Isn’t there supposed to be a built-in reference genome I can select here?
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Welcome, @Maria_F
Please try this tool instead 
bedtools getfasta use intervals to extract sequences from a FASTA file (Galaxy Version 2.31.1+galaxy0)
The Extract tool is a much older UCSC tool and requires a special index format that we are not capturing anymore. The tool above will list all server indexed genomes.
Hope this helps!