When I select the “source of reference genome” as “from history,” it does not show any of the Fasta files I want to use, and then when I force the selection, it writes “(unavailable)” in the file name.
If I try to run, it also writes “Parameter input: Unspecified genome build, click the pencil icon in the history item to set the genome build”.
For the “fetch sequences from intervals in”, I’m using a gff3 file.
Hopefully you found this already but if not, this is what to try instead.
I used that tool at UseGalaxy.org a month ago, and it worked fine with several genomes (how to choose a genome). But if you have trouble, we can follow up more. The server where you are working will matter along with the format of the input GFF3 and the target reference genome. You can post screenshots or share your history to clarify those details and we’ll help to sort out what is going on.
