Homer is wrapped for Galaxy.
You will need to use this in a local or cloud Galaxy. For other analysis, there are a few tools to pick from for comparing peak data, including conversation data (MAF alignments). Galaxy server choices:
For some tutorials to help get oriented, please see:
Galaxy Main: http://usegalaxy.org -> Shared Data: Published Pages/Workflows
Galaxy wiki: http://galaxyproject.org -> Learn, Train
Best, Jen, Galaxy team