Docker Image Update Code - https://bitbucket.org/nzahara/integrated-genome-browser-docker-local/branch/IGBF-2280#diff

IGB Code diff - https://bitbucket.org/noorzahara/integrated-genome-browser-local1/branch/IGBF-2280#diff

To test:

• Check that the IGB branch mentioned above can build under Bitbucket pipelines - look for installers for all platforms in the Downloads section of the fork.
• Check out the branch of the Docker image above. Check that if you run it, the image will be created properly.

(Noor Zahara - please add brief instructions on how to run commands to build the Docker image – for people who might not have used Docker before. If you think this would be easier for them, you can assume the tester is going to build under an Amazon AMI – just specify which one.)

Steps followed to create docker image :

1. Download and install docker software
2. Once Docker file from IGB docker repository has been modified as per the requirement, go to that directory.
3. Build the docker image from docker file using docker build -t <image_name> <path>.
4. run docker ps -a to get the container id.
5. Login to docker hub using the command Docker login -u <username> -p <password>
6. Commit the changes using Docker commit <container-id> <imagename:tag>
7. Finally push the changes - Docker push <imagename:tag>

Note - Testers shouldn't have to push anything to docker hub. The above instructions are for creating a docker image.

Once the installer is installed, 'release' file inside the 'jre' folder can be checked to verify the version.

Noor Zahara Please make a note: tester should not push the image to Docker hub.

Please explain:

Why are there two tagged images on Docker hub:

• jre-1.8.0_241
• jre-8u241

Should one of these be deleted?

jre-8u241 needs to be deleted.

jre-8u241 was created with incorrect bundles.

As part of reviewing this, do please check to see if the bitbucket repository containing the dockerfile has been updated as well.
cc: Shamika Gajanan Kulkarni and Noor Zahara

Yes Prof. [~aloraine]

Reviewed this ticket. The windows installer for this branch is working fine. Also the bitbucket repository containing the dockerfile has been updated. The changes are present in the link mentioned above by Noor Zahara. The installer for mac needs to be verified.

Thank you Shamika Gajanan Kulkarni

Mac installer is working fine.

Thank you Prof. [~aloraine]. I shall move this ticket forward.

PR created -
https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/785/igbf-2280-update-igb-docker-image-to-use/diff

https://bitbucket.org/lorainelab/integrated-genome-browser-docker/pull-requests/4/igbf-2280-update-igb-docker-image-to-use/diff

PR to update Docker image file is merged.

Suggestions on how to test the new docker file:

• Clone latest master - from https://bitbucket.org/lorainelab/integrated-genome-browser-docker
• Use the docker image to create a container on your local or VM
• Run an interactive session and check that you can clone the igb repository and compile IGB using the new JDKs

Suggestions on how to test the new build system:

• Check that the master branch bitbucket file references the "241" docker image.

It seems like the link below, specified in the dockerfile, is not resolvable. The build fails at this step:

https://download-keycdn.ej-technologies.com/install4j/install4j_linux_7_0_8.deb

after some research, the correct url appears to now be:
https://download-gcdn.ej-technologies.com/install4j/install4j_linux_7_0_8.deb

I have updated the install4j url on the branch below:
https://bitbucket.org/pbadzuh/igb-docker_pbdev/branch/IGBF-2280#diff

• the dockerfile now builds successfully
• IGB builds successfully

Thank you so much for catching this error. Please submit PR.

cc Philip Badzuh

Sure! Please see PR below:

https://bitbucket.org/lorainelab/integrated-genome-browser-docker/pull-requests/5/igbf-2280-update-install4j-download-link/diff

Merged and ready for final testing.

To test this, run the docker file and build the image.

Tested on Mac 10.14.6 with Docker 2.1.0.4

Cloned integrated-genome-browser-docker master.

Built Docker image from docker file successfully (docker build --tag nowlandockerigb .).

Ran interactive session locally, able to clone IGB from master, successfully build IGB (mvn clean install).

Moving to Closed.