20 months ago by
Public servers have a fixed set of tools set by the owners/administrators. Tools choices are often based on the available compute these groups have available to share with public users and/or the servers focus on specific analysis pathways. Galaxy Main (http://usegalaxy.org) will not be including HOMER for at least the near term. You can reach out to other groups and ask about their plans directly: PublicGalaxyServers
Setting up a Local Galaxy and adding tools is designed to a be a simple process. The key requirement for successful tool execution is providing enough compute resource. In the most general terms, the resource required by a tool when executed line-command is roughly the same as Galaxy would require to execute it. See any tool's manual for computing requirements (or the tool author's support channels/forums).
The other option is to use a Cloud Galaxy. AWS offers research grants to help with costs.
Both options are covered here: https://wiki.galaxyproject.org/BigPicture/Choices and here https://wiki.galaxyproject.org/Support#About_Galaxy
Hope one of these works out for you! Jen, Galaxy team