Question: Dataset attributes recently messed up?
0
gravatar for jcs92
14 months ago by
jcs9230
United States
jcs9230 wrote:

Hi,

There was an update on Wednesday, and immediately afterwards I've had problems with datasets. It seems that the "edit dataset" tool now mandates filling in fields that don't exist. For example, Refseq gene lists that don't have a field for "visualization." Unless I fill in all fields, whenever I save I get this error: "Error occured while saving. Please fill all the required fields and try again."

Furthermore, simple operations like intersects, which works right before the update, didn't work immediately after.

Any ideas?

attributes galaxy • 614 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by jcs9230

Hi, I'm experiencing the same problem with changes in attributes. Intersect genomic intervals is working for me. Just to add more information,

Hope this gets fixed soon!

Raquel

ADD REPLYlink written 14 months ago by rfabmc10

Yes, there have been changes to reflect the upgrade to Galaxy release 17.09 (pending).

Is this working for you now (resolved the problem with metadata updates)? You could also share a sample of the dataset file and assigned datatype if still having problems.

Intersect genomic intervals requires at least a chrom, start, end, and strand column for an interval format dataset as input.

ADD REPLYlink modified 14 months ago • written 14 months ago by Jennifer Hillman Jackson25k

Yes, there have been changes to reflect the upgrade to Galaxy release 17.09 (pending).

What datatype is your Refseq gene list assign to? Maybe a different datatype would be a better choice? tabular would define just a column list of IDs (one or more)

If the dataset is assigned as bed then it needs to conform to bed format. The "score" would be the 5th column of data.

interval format has more flexible column ordering in general, but certain tools that accept interval format still do require strict bed column ordering.

Datatypes: https://galaxyproject.org/learn/datatypes/

If you cannot figure it out and want to share a sample of your file, the currently assigned datatype, and the tool you want to use it with, that would help to troubleshoot. If there is a problem, we want to review and fix if needed.

ADD REPLYlink modified 14 months ago • written 14 months ago by Jennifer Hillman Jackson25k
2
gravatar for jcs92
14 months ago by
jcs9230
United States
jcs9230 wrote:

I fixed by just adding a strand column and making everything the same strand. I indeed had things in bed format and should get around this by converting to interval.....thanks for your feedback!

ADD COMMENTlink written 14 months ago by jcs9230

Great, glad this worked out!

ADD REPLYlink written 13 months ago by Jennifer Hillman Jackson25k
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