Details
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Type:
Improvement
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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: 10.0.0 Major Release
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Labels:None
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Story Points:3
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Epic Link:
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Sprint:Fall 3 2023 Oct 2, Fall 4 2023 Oct 16, Fall 5, Fall 6, Fall 7
Description
Situation: The BigWigHandler and BigBedHandler have a dependency on the artifact bigWigHandler (https://bitbucket.org/lorainelab/bigwig/src/master/). The bigWigHandler dependency has a dependency on htsjdk-igb version 2.16.2 which makes it a blocker for IGBF-3464.
Task: Fork the bigwig repo and create a new branch with htsjdk-igb updated to a newer version (most likely >= 3). You will need to build and test the dependency locally to make sure that IGB works. See this documentation on adding local jars to local m2 repository.
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Discussed strategy for using newer htsjdk code in IGB. Made a diagram showing the strategy on a whiteboard and took a picture of it. Picture is attached for reference.
I was able to get IGB to build and run using htsjdk 2.24.1. After updating the pom.xml files for htsjdk (instead of htsjdk-igb), I added the following to the pom.xml for shared-lib-wrapper:
Under the section "Dependencies which need to be "wrapped" into OSGI bundles"
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
</dependency>
Then within the maven-bundle-plugin <Export-Package> I added
htsjdk.*
There is one error with BaiFileSymLoader and BaiSymLoader for samReaderFactory.open - this may be due to a change for visualizing the bai data by itself in IGB, though I'm not sure.
I commented out the BigBedHandler, BigWigHandler, and bai modules to get around the errors. Everything else seems to be working in IGB.
However, at this time I recommend Kaushik continue his work on updating htsjdk-igb to use the newer version of the htsjdk.
- Forked htsjdk 3.0.0 into my GitHub and made necessary changes to use it as a OSGi bundle
- Both IGB and BigWig are now pulling htsjdk 3.0.0 from my local maven repository
- Ran the application and no issues were found during compile time or runtime
My concerns:
- Cherry-picking commits can be time-consuming and often leads to dealing with merge conflicts. As a result, I manually incorporated the changes made by the IGB developers into my repository instead of using the cherry-picking process.
- Updated htsjdk-igb and bigwig to version 3.0.5 (previously 2.16.2) and 2.0.1 (previously 2.0.0) respectively
- Submitted PR for the same.
Note: This PR cannot be merged until htsjdk-3.0.5 is deployed. COMPLETED
Tested on Mac using strategy described in IGBF-3464. Everything is working correctly. Closing ticket.
Our BigWig/BigBed code currently declares a dependency on https://github.com/lorainelab/htsjdk-igb