Hi all,
over the last month we developed a new version of GATK2 wrappers and are now seeking for testers, users and overall feedback. We are currently targeting GATK 2.8. One of the big issues with GATK2 is the new licence. Because of that we can't install GATK2 with the wrappers, but we hope we have done it as easy as possible to plugin your local installed version. Furthermore, we made it easy to disable the 'call home feature' of GATK2 (if you have a GATK keyfile). Read more about it:
https://github.com/bgruening/galaxytools/blob/master/gatk2/readme.rst
The code is stored here: https://github.com/bgruening/galaxytools/tree/master/gatk2
The ToolShed wrappers can be found here: http://toolshed.g2.bx.psu.edu/view/iuc/gatk2
I would like to thank Jim Johnson, Nicola Soranzo, Dan Blankenberg and the Galaxy Team. If you like the wrappers you know what to do during the next GCC!
If you have feedback or patches please let us know. Thanks, Bjoern