Question: Using Ensembl gene annotation with Galaxy
0
gravatar for matt.chambers42
15 months ago by
matt.chambers4250 wrote:

I'm trying to use ensembl gene annotations for my tool* but I don't understand how to map them to the UCSC dbkeys. There are multiple ensembl releases for each UCSC dbkey. My loc file has the latest ensembl release for each genome assembly/patch and I've tried to map it to the corresponding UCSC dbkey with this loc file:

When I try to run my tool with it, I see the full list from the loc file, but I get an error when executing: An invalid option was selected for builtin, 'GRCh37.p13', please verify. I don't understand where it even gets that value from.

*because building an ensembl annotation by release # is reproducible, unlike UCSC which always returns the latest gene annotations

ensembl ucsc galaxy dbkey • 541 views
ADD COMMENTlink written 15 months ago by matt.chambers4250
2
gravatar for matt.chambers42
15 months ago by
matt.chambers4250 wrote:

It seems that I only got this error when overriding the preselected value from the workflow. When I edited the workflow to select a different value, the workflow submitted properly. This is with Galaxy 17.05.

ADD COMMENTlink written 15 months ago by matt.chambers4250

This was your own tool? Do you consider this resolved?

Or, have you noticed this behavior with other tools (runtime database changes triggering errors)?

I'll test a few tools as well to see if I can reproduce. If there is a workflow functionality problem we'll want to fix it.

ADD REPLYlink written 15 months ago by Jennifer Hillman Jackson25k

Yes, now I know where the bogus value came from. It was in my workflow .ga file that I imported. That value no longer existed in the loc file. But even when I overrode the value in the workflow run options, it still said invalid option. So it does seem like a UI bug. You should be able to reproduce by editing a .ga file and putting in a bogus value for a genome build parameter (then importing that workflow, running it, and trying to override the bogus value with a valid one).

ADD REPLYlink modified 15 months ago • written 15 months ago by matt.chambers4250

Ok, the explanation helps. I wasn't able to reproduce a problem when switching databases during workflow execution.

I am not sure how often this would come up but tracking the problem seems worth it, as it is confusing to have a genome that is not the selected genome (at runtime) tossing the error. Would you like to open an issue ticket for this use case? This is the correct repository: https://github.com/galaxyproject/galaxy/issues.

Thanks! Jen, Galaxy team

ADD REPLYlink written 15 months ago by Jennifer Hillman Jackson25k
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