I just added the Schizosaccharomyces_pombe_1.1, sacCer2, sacCer3 genomes to the test server at https://test.galaxyproject.org/ for the Bowtie2, Tophat(2), and HISAT2 mapping tools.
We are using a new method to add indexes. If you would like to help test these, please give the new indexes a try. Should errors any occur or simply unexpected results, a bug report/shared history link from the test instance would be welcomed.
We'll also test more here and promote to the Main server at http://usegalaxy.org as soon as possible, along with several other genomes that are in our queue.
If you need to use the genome on the Main server immediately, the option to use a Custom reference genome is still an option (this is true for any reference genome/transcriptome). UCSC is often the best source for the fasta version of a genome, if the genome is supported by them, as many ancillary files commonly used with RNA-seq tools will have the same sequence identifiers (example: reference annotation from iGenomes).
Thanks and have a great weekend, Jen, Galaxy team