Tophat now has several of the most recent Chicken builds from UCSC added. Named like galGal3 (with variants), galGal4. Source UCSC main server, from Downloads: http://genome.ucsc.edu.
I found Duck (anaPla1) at the UCSC test browser http://genome-test.cse.ucsc.edu. It may or may not be fully published to their main server. Still, I'll add this to the list of genomes to add next (we can usually obtain the test-only data): Mallard duck Apr 2013 (BGI_duck_1.0/anaPla1)
To track progress, see this ticket. The genome is in the list of the (currently) second to last post. https://github.com/galaxyproject/galaxy/issues/1470
A custom genome is how to use the Duck (anaPla1) data right now. It may be a month at least before this is retrieved, indexed, and added to http://usegalaxy.org by us. Contact UCSC to find out how to gain public access to the anaPla1 genome fasta file for your own upload into a Galaxy history. https://wiki.galaxyproject.org/Support#Custom_reference_genome
Thanks! Jen, Galaxy team