We were finally successful in downloading selected reference genomes as they appear on the Main instance of Galaxy using Rsync. For example, we have successfully downloaded hg19 and it is located on our server in the Galaxy directory. The problem now is we do not know how to get these files to populate the drop-down menus and be available to respective tools. Can we use Data Managers? We have tried, however when we select to get the genome from our server using the correct path and run Data Managers it completes successfully but hg19 still does not appear to be available in the drop-downs for any of the tools. Does anyone know where we are going wrong?