Details
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Type:
Documentation
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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:0.5
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Epic Link:
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Sprint:Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul
Description
The Transcript Isoform App currently cannot build because its POM.xml file was copied over from the experimental apps repository when we created a new repository for it.
For this task, modify the POM file as required to build the app. See other Apps for best practice examples:
To test that the build is working properly, test that you can upload and release the App using the test App Store - https://testappstore.bioviz.org/.
(Ask Loraine to start it if the URL above does not respond.)
Attachments
Issue Links
- relates to
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IGBF-2373 Move transcript isoform App into a separate repository
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1908 [ 17998 ] |
| Rank | Ranked higher |
| Sprint | Summer 2: 22 Jun - 3 July 2 [ 97 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Sprint | Summer 2: 22 Jun - 3 Jul [ 97 ] | Summer 2: 22 Jun - 3 Jul, Summer 3: 3 Jul - 14 Jul [ 97, 98 ] |
| Rank | Ranked higher |
| Assignee | Prutha Kulkarni [ prutha ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Tested on the testappstore and I was able to release the plugin successfully.
Moving the ticket forward to first level review.
| Assignee | Prutha Kulkarni [ prutha ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
My goodness. Such a simple change - my favorite!
Do please submit PR at your earliest convenience.
attn: Prutha Kulkarni
| Assignee | Prutha Kulkarni [ prutha ] |
PR has been submitted for the same.
https://bitbucket.org/lorainelab/transcriptisoform/pull-requests/2/igbf-2434-modify-transcriptisoform-app-pom/diff
| Assignee | Prutha Kulkarni [ prutha ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Sprint | Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul [ 97, 98 ] | Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul [ 97, 98, 99 ] |
| Rank | Ranked higher |
Merged and ready for testing.
Prutha Kulkarni - please provide instructions for testing.
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | To-Do [ 10305 ] |
| Assignee | Prutha Kulkarni [ prutha ] |
Workflow to install Transcript Isoform App:
- Open IGB Plugin manager and click on add new repository.
- Paste "https://bitbucket.org/lorainelab/transcriptisoform/downloads/" link and click on DONE.
- Click on Show Splice Support app and install it.
- Confirm if the installation was successful by clicking "VIEW" menu in IGB. You would see "transcript Isoform" menu in the bottom of the manu option panel. This indicates that the plugin was installed properly.
Workflow to demo Transcript Isoform App:
- Open Arabidopsis thaliana genome
- Under Data Access panel, open an RNA-Seq data set. For examle, if you are running this older version of IGB, open Pollen > RNA-Seq > SM > Reads > Pollen, Alignments.
- Zoom in on a gene that has some introns. Click Load Data to load some read alignments into the browser. If you are using this older version of IGB, use the Advanced Search tab Keyword Search to find genes that have "pollen" in the description. This will ensure you find some genes that are actually expressed in pollen.
- Select a reference track: Choose View > Transcript Isoform > Select Reference Tiers.
What should happen next is that a "chevron" (looks like a "v") should appear above introns in the reference tier wherever there are "gapped" reads that span the intron.
| 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 ] |
| Assignee | Prutha Kulkarni [ prutha ] | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Chester Dias [ cdias1 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Workflow test
Menu item appears as "Transcript Isoform" under the View menu.
Workflow Demo
Attached screenshot of working condition with chevron.
Closing ticket
| Attachment | Screenshot 2020-07-22 at 13.38.13.png [ 14784 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Chester Dias [ cdias1 ] | Prutha Kulkarni [ prutha ] |
I have modified the pom and pushed the changed onto my fork.
Ref: https://bitbucket.org/pkulka10/transcriptisoform/src/IGBF-2434/
In case anybody wants to test then they can refer:
https://bitbucket.org/pkulka10/transcriptisoform/downloads/
I was not able to test it on the testappstore as the instance was not started.
Dr. [~aloraine], could you please switch it on so that I can try uploading the app on the testappstore?