An error occurred while running the tool data manager gatk picard index builder (the only version of the manager 0.0.1) - I was just trying to build the indexes for the GATK tools, and I didn’t succed
Hi @apolitics
This data manager has not been functional for some time now, was based on an earlier version of GATK (2), included a tool dependency model that is not supported anymore, and the tools it was creating indexes for, and this DM itself, are all considered deprecated. None are hosted at any of the public servers for these same reasons.
Understood, thank you!
What about GATK tools version 3 or 4? don’t they need some kind of indexed reference? (are they also deprecated)
There is only one tool right now: GATK4 Mutect2
The wrapper was adapted to use the (mostly) UCSC assembly based existing indexes hosted at public Galaxy servers and available via CVMFS for local servers (how to: Search Tutorials).
If you have more questions, please start up a new topic. You can reference this one by URL for context if related. 
