I'm sorry to post multiple times for the same question. Now I removed all the specifics of my problem and I only want someone to point me to the right documentation. Admins, I know you are busy, but don't you want more people to benefit from this platform?

When galaxy upgraded it started using the tool_shed version of the tool and killed the tools we installed ourselves. Right now we have both versions. How should we manage this situation properly if we don't want the tool_shed version and want to keep using what we had before?

Nate said that MACS came with galaxy before. I didn't know that. From the day we started using MACS it was installed by ourselves. Not sure if that caused the problem.

Thanks,

Rui