Can't uncheck 'Strand Column' box in attributes of interval file and save

Question: Can't uncheck 'Strand Column' box in attributes of interval file and save

2.6 years ago by

jbeagan • 10 wrote:

Hello, I have an interval file uploaded to one of my galaxy histories. This file does not contain strand data, but when I try to uncheck the 'strand column' box and save the attributes, this box always returns as checked. The result is that I cannot meaningfully use this file, because any operation I perform causes errors because it incorrectly incorporates strand info.

Thanks for your help.

interval attributes • 874 views

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modified 2.2 years ago by jcs92 • 30 • written 2.6 years ago by jbeagan • 10

2.2 years ago by

jcs92 • 30

United States

jcs92 • 30 wrote:

This is a really annoying bug. Still exists, and confounds doing intersects. I workaround by using one of the text manipulation functions to edit the strand column in a Bed file to all "+".

ADD COMMENT • link written 2.2 years ago by jcs92 • 30

Yes, the issue is still open. Thanks for posting the additional workaround! Jen, Galaxy team https://github.com/galaxyproject/galaxy/issues/2175

ADD REPLY • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

2.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I am unable to reproduce this behavior at Galaxy Main http://usegalaxy.org.

If you are working there and would like to share your history with the dataset for review, we can take a look at your exact example. Include the interval dataset's number and a link to this Biostars post along with the shared history link in the email. It is best to share a small history with just the problem dataset and perhaps a few of the failed tools run that used it (copy these datasets over to a new history if needed). Make sure that all datasets are undeleted. Send to: galaxy-bugs@lists.galaxyproject.org

If you are working somewhere else, there could be many other root causes of the problem. You can try to reproduce at http://usegalaxy.org. If you can, submit as above. If you cannot, contacting the administrator of that instance is the best path for a solution.

How to share a history: https://wiki.galaxyproject.org/Learn/Share

Thanks, Jen, Galaxy team

ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks for sending in the shared history. From what I can tell, there is a new metadata problem. The issue was reported to our team for a correction here, along with the work-around (upload the data again): https://github.com/galaxyproject/galaxy/issues/2175

I used part of your original data, but abstracted it using just first ten lines, to protect your data privacy. I couldn't figure out how to reproduce this another way easily and there may be something associated with these specific datasets that is triggering the issue. Our team will want to review that.

Thanks again! Please follow the ticket above for progress on the fix. Jen

ADD REPLY • link modified 2.2 years ago • written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

Hello,

Was this issue ever resolved? I am trying to intersect different datasets again today and having the same issue.

Thanks very much,

Jon Beagan

ADD REPLY • link written 2.5 years ago by jbeagan • 10

Hello, I am having the exact same problem. One thing I've noticed that at least for me, the problem occurs when I try to rename files. If I leave the file with whatever name Galaxy gives it, the strand box remains unchecked. But if I rename it, the box becomes checked and cannot be unchecked.

ADD REPLY • link written 2.6 years ago by zachary.gaber • 80

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