Hi Scott,

It is likely that the bahavior you are experiencing is due to a bug in the 
Workflow framework, so I’d advise submitting an issue describing the problem 
here 
https://github.com/galaxyproject/galaxy/issues<http://github.com/galaxyproject/galaxy/issues>
 if the behavior is different than that described in this existing issue: 
https://github.com/galaxyproject/galaxy/issues/1881.

This will be the best path toward getting a fix.  Sorry I cannot be of more 
help, but I am not an expert with the core Workflow framework.

Greg Von Kuster

On Apr 18, 2016, at 11:56 AM, Scott Szakonyi 
<scott.b.szakony...@nd.edu<mailto:scott.b.szakony...@nd.edu>> wrote:

Hi Greg,

That does look quite similar, but the workarounds presented are not solving the 
issue for us. If you can offer any additional strategies, I would truly 
appreciate it.

Best,

Scott

On Fri, Apr 15, 2016 at 10:56 AM, Von Kuster, Greg 
<g...@psu.edu<mailto:g...@psu.edu>> wrote:
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><mailto: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/><http://crc.nd.edu/>
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--
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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