Hi Scott,

I’m not positive, but this behavior may be related to this issue:

https://github.com/galaxyproject/galaxy/issues/1881

Greg Von Kuster

On Apr 15, 2016, at 10:52 AM, Scott Szakonyi 
<scott.b.szakony...@nd.edu<mailto:scott.b.szakony...@nd.edu>> wrote:

Hello all,

We have indexed a genome using the appropriate data manager, for GATK, and our 
reference is showing up and working for individual walkers in GATK 2.8.  When 
designing a workflow, however, the reference genome is not appearing as an 
option for many walkers, including indel realigner and realigner target 
creator.  It is appearing for haplotype caller.  Again outside of the workflow 
environment the indexed references show up for all walkers.

Any thoughts on this issue?

Thanks!

--
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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