I tried to install galaxy tool (freebayes package) to local incidence. This package has two tools: BamLeftAlign and Feebayes. Strangely, I see one tool (bamleftalign) installed but not the other. The latter tool is functional in galaxy main, so it does not appear that this tool is retired or deprecated. In manage metadata, the latter tool is shown as invalid tools, but not the former. Any helpful comments or possible solution?
I tried to update to the latest version as you suggested. It throws an error:
config/galaxy.ini.sample: needs merge error: you need to resolve your current index first
I did manage to convert galaxy.ini using the command "make config-convert" to yaml file. I am still getting the same error message.