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: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul
Description
Update Docker image - https://bitbucket.org/lorainelab/integrated-genome-browser-docker/src/master/
Also, upload new JDKs to https://bitbucket.org/lorainelab/jre-bundles-install4j/downloads/
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1531 [ 17617 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Comment |
[ [~aloraine] - Can I upgrade JDK to 1.8 release 242 ?
This is the latest version. ] |
| Sprint | Spring 4 : 2 Mar to 13 Mar [ 89 ] | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 89, 90 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Story Points | 1 | 2 |
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.)
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
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.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
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?
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
jre-8u241 needs to be deleted.
jre-8u241 was created with incorrect bundles.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Sprint | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 89, 90 ] | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10 [ 89, 90, 91 ] |
| Rank | Ranked higher |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
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.
| Sprint | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10 [ 89, 90, 91 ] | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr [ 89, 90, 91, 92 ] |
| Rank | Ranked higher |
Thank you Prof. [~aloraine]. I shall move this ticket forward.
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] | Shamika Gajanan Kulkarni [ shamika ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] | Noor Zahara [ noor91zahara ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
PR to update Docker image file is merged.
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Assignee | Ann Loraine [ aloraine ] |
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.
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Sprint | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr [ 89, 90, 91, 92 ] | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May [ 89, 90, 91, 92, 93 ] |
| Rank | Ranked higher |
| Sprint | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May [ 89, 90, 91, 92, 93 ] | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May [ 89, 90, 91, 92, 93, 94 ] |
| Rank | Ranked higher |
| Sprint | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May [ 89, 90, 91, 92, 93, 94 ] | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun [ 89, 90, 91, 92, 93, 94, 95 ] |
| Rank | Ranked higher |
| Sprint | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun [ 89, 90, 91, 92, 93, 94, 95 ] | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun [ 89, 90, 91, 92, 93, 94, 95, 96 ] |
| Rank | Ranked higher |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
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
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
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
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Ann Loraine [ aloraine ] |
Thank you so much for catching this error. Please submit PR.
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Ann Loraine [ aloraine ] | Philip Badzuh [ pbadzuh ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
Merged and ready for final testing.
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Comment | [ Deployed to https://test.bioviz.org. ] |
To test this, run the docker file and build the image.
| Assignee | Nowlan Freese [ nfreese ] |
| Sprint | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun [ 89, 90, 91, 92, 93, 94, 95, 96 ] | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 July [ 89, 90, 91, 92, 93, 94, 95, 96, 97 ] |
| Rank | Ranked higher |
| Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] |
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).
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Moving to Closed.
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
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