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: 10.1.0
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Labels:None
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Story Points:5
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Epic Link:
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Sprint:Spring 8, Spring 9
Description
Task: Update the HTSJDK to the most recent version (see https://github.com/samtools/htsjdk/releases). Currently the Loraine Lab has its own version of the HTSJDK. As part of this ticket, investigate whether we can switch to using the official HTSJDK.
Note that HTSJDK versions greater than 4 are officially compatible with JDK 17. IGB uses JDK 21 so we may encounter some issues upgrading.
Attachments
Issue Links
Activity
- BIGWIG: Upgraded many things, such as HTSHDK, Java, Gradle, and other dependencies in the BigWig Project. Gradle upgrade led to changing some of the APIs in the build.gradle file. BigWid build was successful.
- IGB: the build was successful after upgrading the HTSJDK and BigWig ( which uses HTSJDK and Java 21) versions. However, IGB is throwing bundle exceptions while running the project.
- Will continue to work on resolving issues that occurred after the upgrade.
Instructions for testing:
- fetch this bigwig branch into your local.
- clean the.m2, local maven repository, before you execute the following commands:
Build and install artifact to local
./gradlew clean build
./gradlew publishToMavenLocal
Note: For Windows, use gradle.bat file instead of gradlew.
- fetch this IGB branch into your local. This branch uses Samtools htsjdk 4.1.0 and bigwig 3.0.0 (uses htsjdk 4.1.0 and jdk 21) dependencies.
- Maven commands
mvn clean build
- run the IGB, and while testing, monitor the logs. Test bam, sam, cram, bigbedhandler, and bigwighandler features, as these plugins use htsjdk and bigwig dependencies.
Question for Nowlan Freese
- With this upgrade, IGB no longer supports the BAI feature. How would you like to proceed with the BAI plugin further? Do you want to delete (or) disable it? Let me know your thoughts.
My steps for testing:
For BigWig: I fetched Kaushik's bigwig branch. I needed to upgrade my gradle in order to build (now at 8.7).
brew upgrade gradle gradle clean build gradle publishToMavenLocal
I then fetched Kaushik's IGB 3671 branch.
I tested all of the files in the smoke testing quickload, including bigwig, bigbed, bam, sam, cram, and vcf. All files loaded as expected, no errors in the logs.
Next step: I want to double check with Kaushik that we have the versioning of the bigwig artifact correct before deploying. Otherwise everything appears to be working.
BigWig pull request - https://bitbucket.org/lorainelab/bigwig/pull-requests/4
Update:
- PR is merged. Proceeding with building new artifact.
- Built it with:
local aloraine$ gradle clean build
Starting a Gradle Daemon (subsequent builds will be faster)
> Configure project :
Java Version: 21.0.2 (BellSoft 21.0.2+14-LTS)
> Task :compileJava
Note: /Users/aloraine/src/bigwig/src/main/java/org/broad/igv/bbfile/BPTree.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
BUILD SUCCESSFUL in 13s
4 actionable tasks: 4 executed
local aloraine$
- Manually uploaded artifacts to maven.bioviz.org as version 3.0.0
Bigwig 3.0.0 artifact available from https://nexus.bioviz.org/repository/maven-releases/org/broad/igv/bigwig/3.0.0/bigwig-3.0.0.jar
PR is merged and new "main branch" installers are built. Also, I have deployed the new installers to the "igb early access" section of bioviz.org.
The project pom.xml for the main branch now uses htsjdk version 4.1.0 and the bigwig version 3.0.0. I was able to load bam/sam/bigwig/bigbed without issue.
Closing ticket.