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:1
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Epic Link:
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Sprint:Summer 1, Summer 2, Summer 5, Summer 6, Summer 7
Description
Three additional tasks to update / improve the find junction code in bitbucket:
1) Now that find junctions is recommended to be built using JDK 21, we need to update the bitbucket pipelines file. The pipeline might not even run, so this task may take some effort to debug it.
2) Also, we may also want to indicate in the README which genome a user needs to open in order to view the "test" bed file, and explain to the user what they ought to see in IGB when they do that. That way, if there is a problem, they will know.
3) Lastly, let's change the main development branch from "master" to "main".
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Summary | Update find junctions repository bitbucket pipelines file | Update find junctions repo even more - main branch, bitbucket pipeline, more readme text |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Summer 1 [ 195 ] | Summer 1, Summer 2 [ 195, 196 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Updated the pom.xml and bitbucket-pieplines.yml files to use jdk 21 instead of 1.8. Updated code is at the branch: https://bitbucket.org/jaya-sravani/findjunctions/branch/IGBF-3738. The jar is built successfully in Bitbucket as well. Please review and let me know if there are any issues.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Sprint | Summer 1, Summer 2 [ 195, 196 ] | Summer 1, Summer 2, Summer 3 [ 195, 196, 197 ] |
| Rank | Ranked higher |
Thanks for the changes. These look good. Please submit PR when ready.
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
Raised a Pull request: https://bitbucket.org/lorainelab/findjunctions/pull-requests/2
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
PR is now merged. Ready for testing.
The pipeline runs and the jar file is built.
There are still two new tasks to be done - see description.
Moving this to To-Do but out of the current sprint as these changes are not super high priority.
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
| Sprint | Summer 1, Summer 2, Summer 3 [ 195, 196, 197 ] | Summer 1, Summer 2, Summer 4 [ 195, 196, 198 ] |
| Sprint | Summer 1, Summer 2, Summer 4 [ 195, 196, 198 ] | Summer 1, Summer 2, Summer 5 [ 195, 196, 199 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
Updated the README.md file to include the visualize data steps, updated code is present at: https://bitbucket.org/jaya-sravani/findjunctions/branch/IGBF-3738. As I don't have permission to create a new branch in the loraine lab workspace, I am thinking of creating a new main branch from the master branch in my workspace and then pushing it to the loraine lab workspace, this can be done once the above changes are also merged. Please review and let me know if there are any changes required.
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Summer 1, Summer 2, Summer 5 [ 195, 196, 199 ] | Summer 1, Summer 2, Summer 5, Summer 6 [ 195, 196, 199, 200 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
If you are able to create a new branch "main" from "master", that would be awesome. The instructions look good - no changes requested.
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Ann Loraine [ aloraine ] | Jaya Sravani Sirigineedi [ jsirigin ] |
Raised the pull request: https://bitbucket.org/lorainelab/findjunctions/pull-requests/3, please review and let me know if there are any issues.
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
PR is merged. Also please note that I have changed to default branch to "main" instead of "master".
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Summer 1, Summer 2, Summer 5, Summer 6 [ 195, 196, 199, 200 ] | Summer 1, Summer 2, Summer 5, Summer 6, Summer 7 [ 195, 196, 199, 200, 201 ] |
| Rank | Ranked higher |
Note that the built jar file in the Downloads requires JDK 21 now. I noticed this when I
Has anyone tried running the newly build jar file? I tried it on the UNC Charlotte cluster, but the JVM I usually use would not run it because the java versions did not match up.
To test that the code is still runnable, someone needs to actually try running the find-junctions.jar artifact.
To do this:
1) Download the jar file from https://bitbucket.org/lorainelab/findjunctions/downloads/find-junctions-1.0.0-jar-with-dependencies.jar
2) Follow the instructions in the 'readme" file to test-run the code
Request for Nowlan Freese or Dylan Marrotte: Would one of you be able to do the above testing?
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Assignee | Nowlan Freese [ nfreese ] | Paige Kulzer [ pkulzer ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
With JDK 21 installed on my computer, I downloaded the jar file from the link above and tested the code using the instructions in the "readme" from the FindJunctions repo. The modified readme was easy to follow and straightforward. The test files (1.bam and test.bed) loaded into IGB properly and at least one junction is present in the test.bed track.
Moving this to Done.
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Paige Kulzer [ pkulzer ] | Jaya Sravani Sirigineedi [ jsirigin ] |
Changed the JDK version to 21 in my local and built the application, jar is generated successfully. Modified the bitbucket pipeline code too, will test this once my build minutes are renewed.