Hi Scott,

as far as I know the GATK wrappers > 3.4 are community maintained, there
is not much we can do for you here.

I personally stopped to work on GATK because of the license issues and
all I know is that the iuc/devteam datamanager worked for GATK2.8.

Sorry,
Bjoern

Am 01.03.2016 um 13:52 schrieb Scott Szakonyi:
> Hi all,
> 
> Sorry to be repetitive, but this issue is really blocking our efforts to
> develop the workflow that we need in our instance of Galaxy. If anyone
> has any familiarity with the issue described below, please let me know.
> I really need to get this solved.
> 
> One of my co-administrators is having some issues with data
> indexed/processed with data managers in GATK. His email to me:
> 
> 
>     Currently there is no way to load a genome into versions of GATK
>     above version 1.4.  No version seems to be able to load a reference
>     from history and only version 1.4 seems to work with the available
>     picard-gatk data manager.  We need to be able to work with these
>     later versions of GATK, 3.4 on the Galaxy tool shed is the latest.  
> 
> 
> Thanks!
> 
> Scott
> -- 
> Scott B. Szakonyi
> Research Programmer
> 
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu <http://crc.nd.edu/>
> 
> 
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