[IGBF-3705] Add USEQ support back to IGB - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: 10.1.0
Labels:
None

Story Points:
5
Epic Link:
Improve IGB for users
Sprint:
Spring 10, Summer 1

Description

Situation: A user has reported that they are unable to load USEQ files in IGB in 10.0.0. We removed USEQ support in IGB 9.1.10 (~~IGBF-3146~~).

Task: Add USEQ support back to IGB. It was removed in this pull request.

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chr17_H_sapiens_Mar_2006_Graph.useq
24/May/24 2:34 PM
44 kB
Nowlan Freese
chr17_H_sapiens_Mar_2006_Region.useq
24/May/24 2:34 PM
12 kB
Nowlan Freese
chr17_H_sapiens_Mar_2006_StrandedReadCoverage_Graph.useq
24/May/24 2:34 PM
611 kB
Nowlan Freese
Screenshot 2024-06-04 at 2.37.09 PM.png
04/Jun/24 3:40 PM
244 kB
Jaya Sravani Sirigineedi
Screenshot 2024-06-04 at 3.35.26 PM.png
04/Jun/24 3:40 PM
224 kB
Jaya Sravani Sirigineedi
Screenshot 2024-06-04 at 3.39.38 PM.png
04/Jun/24 3:40 PM
229 kB
Jaya Sravani Sirigineedi
useqBroken.png
24/May/24 2:55 PM
171 kB
Nowlan Freese
useqWorking.png
24/May/24 2:55 PM
162 kB
Nowlan Freese

Issue Links

relates to

IGBF-3146 Remove "useq" packages from genometry bundle in IGB

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Nowlan Freese added a comment - 24/Apr/24 10:07 AM

User conversation:

I have updated to ver.10.0.0. But it could not apply .useq file and it shows "FORMAT NOT RECOGNIZED".
I also tried to upload .useq file which could upload previously, but same error message displayed.
I checked "Species" and "Genome version". What was wrong? Is there any suggestions?
Thanks,
Sachi

Hi Sachi,

USEQ support was removed in 2022 for IGB 9.1.10. I will look to see if we can add USEQ support back to IGB for the next release. In the meantime, I would suggest downloading IGB 9.1.8 from SourceForge and install it on your computer as it should be the most recent version of IGB to support USEQ: https://sourceforge.net/projects/genoviz/files/IGB%209.1.8/

Sorry for the trouble!

Nowlan

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Nowlan Freese added a comment - 24/Apr/24 10:07 AM User conversation: I have updated to ver.10.0.0. But it could not apply .useq file and it shows "FORMAT NOT RECOGNIZED". I also tried to upload .useq file which could upload previously, but same error message displayed. I checked "Species" and "Genome version". What was wrong? Is there any suggestions? Thanks, Sachi Hi Sachi, USEQ support was removed in 2022 for IGB 9.1.10. I will look to see if we can add USEQ support back to IGB for the next release. In the meantime, I would suggest downloading IGB 9.1.8 from SourceForge and install it on your computer as it should be the most recent version of IGB to support USEQ: https://sourceforge.net/projects/genoviz/files/IGB%209.1.8/ Sorry for the trouble! Nowlan

6 older comments

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Nowlan Freese added a comment - 05/Jun/24 4:32 PM

Tested on updated branch, issue is fixed, ready for pull request.

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Nowlan Freese added a comment - 05/Jun/24 4:32 PM Tested on updated branch, issue is fixed, ready for pull request.

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Jaya Sravani Sirigineedi added a comment - 06/Jun/24 10:03 AM

Raised a Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1019. Please review and let me know if there are any issues.

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Jaya Sravani Sirigineedi added a comment - 06/Jun/24 10:03 AM Raised a Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1019 . Please review and let me know if there are any issues.

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Ann Loraine added a comment - 06/Jun/24 11:25 AM - edited

PR is merged. Installers are built and deployed to the "early access" section of bioviz.org web site.

Question for the team: After testing, could we let the user know about the updated IGB version?

Paige Kulzer, Nowlan Freese, Jaya Sravani Sirigineedi

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Ann Loraine added a comment - 06/Jun/24 11:25 AM - edited PR is merged. Installers are built and deployed to the "early access" section of bioviz.org web site. Question for the team: After testing, could we let the user know about the updated IGB version? Paige Kulzer , Nowlan Freese , Jaya Sravani Sirigineedi

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Nowlan Freese added a comment - 06/Jun/24 11:40 AM

Ann Loraine - Yes that is a good idea, I will reach out to them and let them know once it is tested. It would be great if they could try it out as they seem to be very familiar with useq.

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Nowlan Freese added a comment - 06/Jun/24 11:40 AM Ann Loraine - Yes that is a good idea, I will reach out to them and let them know once it is tested. It would be great if they could try it out as they seem to be very familiar with useq.

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Nowlan Freese added a comment - 07/Jun/24 11:30 AM

Tested using early-access installer on Mac.

I was able to load and then remove data from the three test files in IGB successfully with no errors/warnings in the log.

I have also messaged the IGB user through the IGB help desk to let them know about USEQ support in IGB Early Access.

Closing ticket.

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Nowlan Freese added a comment - 07/Jun/24 11:30 AM Tested using early-access installer on Mac. I was able to load and then remove data from the three test files in IGB successfully with no errors/warnings in the log. I have also messaged the IGB user through the IGB help desk to let them know about USEQ support in IGB Early Access. Closing ticket.

Add USEQ support back to IGB

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