GATK2 Galaxy wrapper available, testing and help needed

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GATK2 Galaxy wrapper available, testing and help needed

Björn Grüning-2
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:

The code is stored here:

The ToolShed wrappers can be found here:

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.


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