If i download iGenome of particular species (In may case Chicken) from http://ccb.jhu.edu/software/tophat/igenomes.shtml, after uploading into Galaxy, i can use this genome indexes for my reference genome instead of going to build custom genome reference.
Yes, the content here has both the reference annotation (gtf) and the reference genome (fasta). The fasta can be used as a custom genome. If the target is galGal3, this reference genome is already indexed for HISAT2, so just the gtf would be needed. Also indexed for HISAT2 is galGal4, but I do not believe there is a gtf from iGenomes yet for this build.
Just please be aware the galGal3/galGal4 are not indexed for Tophat (aka Tophat2) and BWA/BWA-MEM for technical reasons that are yet unresolved. These two would probably fail for memory if used as a custom genome at http://usegalaxy.org. The other genome sources may or may not work. If you try any of these and the job fails for memory, then moving to a local or cloud Galaxy with a compute-intensive level of dedicated resource would be the solution (over 64 GB job memory).
Best, Jen, Galaxy team