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: 10.0.0 Major Release
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Labels:None
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Epic Link:
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Sprint:Fall 7, Fall 8, Spring 1
Description
Situation: As part of the migration to JDK21 we are also updating the Docker image to use Install4J v10.
Task:
- Create the IGB Docker image used in Bitbucket pipeline to use Install4J v10 with our JRE bundles for Linux, Mac ARM (ARCH64), Mac Intel (AMD64), and Windows.
- Confirm that the Docker image can build installers using Bitbucket pipeline
- Update the documentation as required in the IGB Docker repository: https://bitbucket.org/lorainelab/integrated-genome-browser-docker/src/master/
- Confirm that the new Dockerfile can properly create the Docker image using a Loraine Lab VM in AWS (see: https://bitbucket.org/lorainelab/bioviz-playbooks/src/master/docker.yml - note: this may also need updating and documentation)
- Once all of the above has been done, push our new Docker image to the Loraine Lab Docker hub account with the correct tag
Note that DCN has already created a Docker image which we've been testing with our Bitbucket pipeline.
Attachments
Issue Links
- relates to
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IGBF-3521 Investigate build problem: effective model for org.lorainelab.igb:affymetrix-common:bundle:10.0.0
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- To-Do
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Activity
Made branch IGBF-3508 on my fork https://bitbucket.org/aloraine/integrated-genome-browser to fix the above-mentioned error.
Cloned my new branch onto the docker host (as ec2-user) with
git clone --single-branch --branch IGBF-3508 https://bitbucket.org/aloraine/integrated-genome-browser build
As ec2-user, started interactive docker container session with:
docker run -i -t -v ~/build:/build --env-file env_vars --workdir /build igb-maven-install4j:I4J10-jre-21.0.1-21.0.0 /bin/bash
Inside container, attempted built installers with:
mvn install -P release-bitbucket-pipelines
Downloaded MacOS installer to my computer and ran it. Observed that IGB started.
Because the Docker image was able to build a working MacOS installer, re-tagged the new image with:
docker.bioviz.org ec2-user $ docker tag f0a8b3d62078 lorainelab/igb-maven-install4j:I4J10-jre-21.0.1-21.0.0
Confirmed the tag with:
docker.bioviz.org ec2-user $ docker image ls REPOSITORY TAG IMAGE ID CREATED SIZE lorainelab/igb-maven-install4j I4J10-jre-21.0.1-21.0.0 f0a8b3d62078 15 minutes ago 2.86GB igb-maven-install4j I4J10-jre-21.0.1-21.0.0 f0a8b3d62078 15 minutes ago 2.86GB <none> <none> 4e0fb64a282f 19 hours ago 2.86GB igb-maven-install4j I4J10-jre-21.0.1 91f23d890b25 4 weeks ago 2.86GB igb-maven-install4j I4J10-nonuniversal-full-jre-21.0.1 2e7cb3f63270 5 weeks ago 4.12GB lorainelab/igb-maven-install4j I4J10-nonuniversal-full-jre-21.0.1 2e7cb3f63270 5 weeks ago 4.12GB
Logged into our docker hub account with:
docker login -u aloraine
Pushed new image with:
docker push lorainelab/igb-maven-install4j:I4J10-jre-21.0.1-21.0.0
Confirmed that the image is properly uploaded by seeing it listed here: https://hub.docker.com/r/lorainelab/igb-maven-install4j/tags
Updated bitbucket pipeline configuration file to use the new image. Committed the change to my branch IGBF-3508 and pushed to fork.
The push triggered pipelines to build the new installers. Installers are available in the fork's Downloads section here: https://bitbucket.org/aloraine/integrated-genome-browser/downloads/
Downloaded MacOS installer and confirmed it could run on my Big Sur Intel MacOS computer.
Submitted PR from my fork and branch to target branch main-JDK21-with-javafx-no-theme on the team repository.
Merged the PR with the target branch main-JDK21-with-javafx-no-theme.
Launched pipeline to build branch installers as usual.
Installers are built and ready for testing.
See:
- https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/IGB-macos-universal-main-JDK21-with-javafx-no-theme.dmg
- https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/IGB-windows-main-JDK21-with-javafx-no-theme_amd64.exe
- https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/IGB-linux-main-JDK21-with-javafx-no-theme_amd64.sh
Note: Also, updating dockerfile and pushing to repository lorainelab/integrated-genome-browser-docker.git.
Tested installer and IGB on MacOS 13.6.3 and Windows 10 - both worked successfully.
The installer worked on MacOS 14.2.1. I also tested the installer on Windows 11 which seemed to work, though I did not get a chance to open IGB and check its functionality before my laptop died.
Pushed new Dockerfile to https://bitbucket.org/lorainelab/integrated-genome-browser-docke branch jdk21.
Moving to DONE because all the code has been tested and all is fine.
We were seeing an error when running the pipeline where libfontmanager.so is missing from Install4Jv10's own JRE (downloaded the Install4Jv10 debian distribution). Install4J is using a version of JDK17 that is missing libfontmanager.so. David removed their JRE and added a different JRE 17 for Install4J to use (you can see this in the Docker file). So this is why there are two JREs being installed onto the Docker Image. We also had to install a fontmanager/config on the Docker image for Install4J to work correctly.