Is it possible to integrate Bismark aligner as a plug-in in Galaxy? It is already in Galaxy toolshed but I don't know how to run the local Galaxy as administrator so it would be very useful to have it integrated into the public Galaxy for researchers like me who is willing to analyze methylation data.
Can Küçük, Ph.D.
There are no plans to add this tool to the public Main Galaxy instance at http://usegalaxy.org at this time. However, the instructions to build up a local or cloud Galaxy include setting up as admin so that tools can be installed is described a few simple steps in our wiki (Cloudman is probably needed, unless you have enough job resources locally).
You could also check the public servers list to see who is hosting the tool at this time publically, but often these sites have smaller quotas for external users that Main. So small jobs may work, but large will not.
Thanks, Jen, Galaxy team