This genome is already on our next list of genomes to process, the card is here: http://trello.com/c/YqRsZnFI
Meanwhile, you can use the genome right now as a Custom Reference Genome.
In short, load the genome in fasta format into your history and use it with the tool settings to use a reference genome "from the history".
The "danRerN" genomes on the public server are sourced from UCSC here:
Or you can obtain our exact version from our rsync server:
Best, Jen, Galaxy team