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
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.Szakonyi.1@nd.edu<mailto:Scott.B.Szakonyi.1@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/> ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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 <ghv2@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.Szakonyi.1@nd.edu <mailto:Scott.B.Szakonyi.1@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/> ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu
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.Szakonyi.1@nd.edu<mailto:Scott.B.Szakonyi.1@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 <ghv2@psu.edu<mailto:ghv2@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.Szakonyi.1@nd.edu<mailto:Scott.B.Szakonyi.1@nd.edu><mailto:Scott.B.Szakonyi.1@nd.edu<mailto:Scott.B.Szakonyi.1@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/> ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- 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/>
participants (2)
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Scott Szakonyi -
Von Kuster, Greg