Docker file changes

https://bitbucket.org/nzahara/integrated-genome-browser-local/branch/IGBF-1840#diff

Docker file repo:

• https://bitbucket.org/lorainelab/integrated-genome-browser-docker/src/master/

JRE repo:

• https://bitbucket.org/lorainelab/jre-bundles-install4j

[~aloraine]

Problem Exists with windows parent version 1.8 and Windows Scaling (Breaks if scaling is more than 100%)

Ticket:

https://bugs.openjdk.java.net/browse/JDK-8180815

Please look at the close statement.

PS: Attached Screenshot with Problem Resolution

Tried upgrading JDK/JRE to 9.0.1 but getting an error as attached while installing IGB. The branch was successfully built.

Used openjdk as well but javafx libraries are not supported.

For the next steps:

• Upload all the JREs used to make the new Docker image to the JRE repo (see link above)
• Submit a pull request to update the docker file showing the changes made to make the new Docker image - use fork-and-branch workflow as with IGB (see link above)

To test new Docker image:

• Create a branch in integrated-genome-browser repository that edits the Docker file referenced in bitbucket pipelines YML file
• Push branch to a fork
• Check that the project builds and artifacts are correctly copied to fork's download location
• Download and run installers for each platform
• Confirm IGB runs as expected; check Console for error messages, esp. ClassNotFound errors or OSGi wiring errors

One way to solve the issue manually is by following the below steps:

Right click on the application icon and click “Properties.”
Go over to the Compatibility tab, enable “Override High DPI scaling behavior” and set the Scaling Behavior to “System (Enhanced).”

[~aloraine]

Docker file changes can be found here : https://bitbucket.org/noorzahara/integrated-genome-browser-docker-local/branch/IGBF-1840#diff

IGB Code changes : https://bitbucket.org/noorzahara/integrated-genome-browser-local1/branch/IGBF-1840#diff

Steps to create a JRE Bundle

1. Download jre fom Oracle.
2. Unpack the file.
3.Install install4j on respective platforms
4.Open install4j and then click on Project -> Create JRE Bundle
5.Upload the unpacked jre file and create a bundle.

There were a lot of moving parts here – 3 bitbucket repositories and a Docker hub repository. Because this is unusually complicated, let's back up and do a first level review.

To get fresh eyes, please request help from the CyVerse team.

Suggestions for code review:

1. Check that the requested Docker image is available from lorainelab docker hub account.
2. Check that there the Dockerfile for same has been updated (or there is a pull request in the queue to update it)
3. Compare requested code changes for updating the JRE in the install4j and bitbucket pipelines files to what was done before - check for any differences.

Suggestions for functional review:

1. Download and run each installer on Mac, Windows, Linux
2. Inspect the installed version. Try to confirm it's the expected JRE.

As always, please add comments to indicate what testing was done and if testing passed.

Confirming Code review item 2 above:

• Pull request for updating the Docker file has been submitted and merged. See: https://bitbucket.org/lorainelab/integrated-genome-browser-docker

We've made some changes to the POMs that unfortunately conflict with your branch.
Can you rebase your branch? Sorry, it may be a bit tricky to do it!

[~aloraine]

I have pulled the latest code from master and also resolved the conflicts

Please check for any new conflicts (since previous resolution) and submit pull request when resolved.

Checked the version on Windows and Mac platforms. The latest version has been updated. Moving to done.