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
- Closed
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IGBF-2777 Fix View Region in UCSC Browser
- Closed
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IGBF-2855 Investigate activating UCSC DAS source from External View tab
- Closed
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IGBF-2869 Investigate adding UCSC JSON API as a new data provider
- Closed
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IGBF-781 Update synonyms.txt for UCSC
- Closed
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HELP-370 UCSC
- Closed
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IGBF-2474 Remove DAS v1 support (UCSC DAS v1 service not responding)
- Closed
Activity
Field | Original Value | New Value |
---|---|---|
Epic Link | IGBF-1765 [ 17855 ] |
Fix Version/s | 9.1.8 Major Release [ 10605 ] |
Summary | Add back DAS support | Restore DASv1 support |
Description |
Situation: A user has asked for the UCSC DAS functionality to be returned to IGB.
Task: Revert the changes to remove DAS support from IGB. |
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. |
Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Assignee | Nowlan Freese [ nfreese ] |
Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Link | This issue relates to HELP-374 [ HELP-374 ] |
Assignee | Rachel Weidenhammer [ rweidenh ] |
Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Status | First Level Review in Progress [ 10301 ] | Needs 1st Level Review [ 10005 ] |
Assignee | Rachel Weidenhammer [ rweidenh ] |
Assignee | Nowlan Freese [ nfreese ] |
Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
Status | To-Do [ 10305 ] | Pull Request Submitted [ 10101 ] |
Assignee | Nowlan Freese [ nfreese ] |
Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Assignee | Philip Badzuh [ pbadzuh ] |
Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Resolution | Done [ 10000 ] | |
Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Assignee | Philip Badzuh [ pbadzuh ] | Nowlan Freese [ nfreese ] |
Resolution | Done [ 10000 ] | |
Status | Closed [ 6 ] | To-Do [ 10305 ] |
Attachment | dasgff.dtd [ 15492 ] |
Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Resolution | Done [ 10000 ] | |
Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Resolution | Done [ 10000 ] | |
Status | Closed [ 6 ] | To-Do [ 10305 ] |
Sprint | Winter 5 Feb 22 - Mar 5 [ 115 ] | Winter 5 Feb 22 - Mar 5, Spring 3 2021 Apr 19 - Apr 30 [ 115, 119 ] |
Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Assignee | Nowlan Freese [ nfreese ] | Omkar Marne [ omarne ] |
Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Assignee | Omkar Marne [ omarne ] | Nowlan Freese [ nfreese ] |
Story Points | 2 | 4 |
Assignee | Nowlan Freese [ nfreese ] |
Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Assignee | Rachel Weidenhammer [ rweidenh ] |
Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Resolution | Done [ 10000 ] | |
Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Assignee | Rachel Weidenhammer [ rweidenh ] | Nowlan Freese [ nfreese ] |
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)