[galaxy-user] Converting VCF to gd_genotype

2014-02-24 Thread Mike Montague 
I'm interested in using the Genomic Diversity tools. I've used these 
with success for a previous project. For this current project, I've 
converted a vcf file (29 subjects) to a gd_genotype file. When I attempt 
to specify individuals, the checkboxes for each subject are not present. 
Without specifying individuals, I am unable to complete other analyses 
(overall FST, etc.)


I cannot distinguish a difference between the vcf files that were 
successful from the previous project and this current project's vcf, but 
I assume there is a format difference that I cannot detect.


I'm using Galaxy at the main site. I executed the jobs on Fri Feb 21 
22:09:49 2014 (UTC). I can share the histories of the projects if necessary.


Mike

--


Michael J. Montague, Ph.D.
Post-Doctoral Research Associate
The Genome Institute, Washington University School of Medicine
 Forest Park Avenue, Campus Box 8501
St. Louis, MO 63108
T. 718.809.4093



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Re: [galaxy-user] Converting VCF to gd_genotype

2014-02-24 Thread Jennifer Jackson 

Hello Mike,

Yes, we have similar recent reports of issues with tools from this group 
and are actively investigating the root cause. It is unknown whether or 
not python version is related, but right now we are tracking the issues 
under a single ticket with that as a suspected contributing factor. You 
can follow this ticket, and any tickets that branch from it, here:

https://trello.com/c/yXrDICmg

Our apologies for the current inconvenience,

Jen
Galaxy team

On 2/23/14 2:40 PM, Mike Montague wrote:
I'm interested in using the Genomic Diversity tools. I've used these 
with success for a previous project. For this current project, I've 
converted a vcf file (29 subjects) to a gd_genotype file. When I 
attempt to specify individuals, the checkboxes for each subject are 
not present. Without specifying individuals, I am unable to complete 
other analyses (overall FST, etc.)


I cannot distinguish a difference between the vcf files that were 
successful from the previous project and this current project's vcf, 
but I assume there is a format difference that I cannot detect.


I'm using Galaxy at the main site. I executed the jobs on Fri Feb 21 
22:09:49 2014 (UTC). I can share the histories of the projects if 
necessary.


Mike



--
Jennifer Hillman-Jackson
http://galaxyproject.org

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Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

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