Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Fall 1 - Sep 5, Summer 5 2023 July 10, Summer 6 2023 July 24, Summer 7 2023 Aug 7, Summer 8 2023 Aug 21, Fall 2 2023 Sep 17
Description
makeAnnotsXml.py needs to be edited so that tomato genome assemblies SL4 and SL5 can be used to visualize all the studies.
The sample sheet being used is KP_sample_sheet.xlsx. Once edits have been made, then run the script to remake Quickload/ directory contents.
Observe that direct links into the repository are being used to serve metadata about the Quickload repository.
Attachments
Issue Links
Activity
Status: I have been reviewing the code and understanding the new objects. I added the bitbucket IGBF-3389 branch URL to IGB. I then added the original URL from main to compare the two.
Comparison:
- There are obviously more folders/data for the branch URL compared to the main URL.
- I chose two reads which came from the branch and main. The data seem to be identical for the original folders and work in IGB on the branch.
- The new folders are also loading data correctly.
- When I change to the SL4 genome there are now only 2 available data sets for the branch, which is true to the code.
- When I also changed to SL4 the main URL doesn't have SL4 data available
Notes: I believe the new branch works and provides a great adaptation for viewing the SL4 genome versions of the data that have been processed. I need to review the code some more to determine that all of the new objects are working like they should.
PR merged.
To test, check that you can visualize the data after adding the newly merged data source to IGB, following the directions in the "README.md" at https://bitbucket.org/hotpollen/genome-browser-visualization/src/main/.
This is now the "production" or "released" version of the "hotpollen" IGB quickload site.
Testing:
- I used the main URL from the README and added the quick load source to IGB
- Opened tomato genome for SL5 and all of the folders seem to be present
- The data files from SL5 load properly in IGB and are visually correct
- When I switch to the SL4 genome now only two folders are present which is accurate to the script/code
- When I try to load any of the SL4 data and view it in IGB I run into an issue:
The feature https://data.bioviz.org/hotpollen/S_lycopersicum_Sep_2019/muday-2022-timeseries/7-are-15-min-28C.scaled.bedgraph.gz is not reachable. More information about what went wrong may be available in the Console. To get help, visit the IGB Help Page.
URL not reachable
Comment: I believe this is because this data on bitbucket is locked so that is why the link isn't working in IGB. This is true for Muday lab (PT time GM lab) and Ravi lab (RP lab pilot). This issue has been acknowledged before but was only fixed for SL5. In other words, the URL's for locked repos, Muday and Ravi, work for the SL5 genome but not the SL4 genome.
Thank you for finding these errors [~molly].
I had forgotten to change the permissions of directories and files to make them all world-readable. This is now fixed. Ready for testing again.
Testing:
- I used the main URL from the README and added the quick load source to IGB
- Opened tomato genome for SL5 and all of the folders seem to be present
- The data files from SL5 load properly in IGB and are visually correct
- When I switch to the SL4 genome now only two folders are present which is accurate to the script/code
- With the new update I can now load SL4 data
Moving to done!
Also am including the Arabidopsis June 2009 genome.