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: 9.1.8 Major Release
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Labels:None
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Story Points:4
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Epic Link:
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Sprint:Winter 5 Feb 22 - Mar 5, Spring 3 2021 Apr 19 - Apr 30
Description
Situation: A user has asked for the UCSC DAS functionality to be returned to IGB.
Task: Revert the changes to remove DASv1 support from IGB.
Attachments
Issue Links
- relates to
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IGBF-2776 Fix External View tab
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- Closed
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- Closed
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- Closed
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- Closed
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IGBF-781 Update synonyms.txt for UCSC
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- Closed
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- Closed
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- Closed
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Activity
To test, download IGBF-2793 installer.
In IGB with UCSC DAS enabled:
Select the Caenorhabditis brenneri in the Species dropdown
Select the C_brenneri_Feb_2008 Genome Version
Navigate to Un:55,401,094-55,401,137
Click Load Sequence
The sequence should appear if working correctly.
The sequence appeared as expected.
Merged to master branch and built master branch installers. Ready for testing.
Tested on Windows.
sequence loads.
UCSC (DAS) appears in the Data Access panel and those files load as well.
moving to closed.
Branch: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-2793
To test:
Open the mouse genome (M_musculus_Dec_2011)
Navigate to chr1:52,182,882-52,235,630
Select the External View tab
In the dropdown menu, select UCSC (should be UCSC by default)
Click update (Gene annotations should appear in the External View tab)
Next, select View > View Region in UCSC Browser (a web browser should open to genome.ucsc.edu)
Next, select the Data Access tab
Under Available Data, there should be a folder for UCSC (DAS)
Click the arrow to see all of the options under UCSC (DAS)
Select ncbiRefSeqCurated (note that the DAS menu and data may move slowly as they utilize an external resource)
Once the track has appeared in IGB, click Load Data (gene models should appear)