Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Blocker
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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:
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Story Points:2
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Epic Link:
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Sprint:Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 4 2021 May 3 - May 14, Summer 1 2023 May 15, Summer 2 2023 May 29, Fall 3 2023 Oct 2, Spring 5, Fall 4, Fall 5, Fall 6, Fall 7
Description
Read modules 2 and 3 the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers.
To build IGB installers:
- Log in to bitbucket using your bitbucket user account.
- Check your account has been added to the Developers group by confirming that you can open and see private (as denoted by a "padlock" icon) IGB project repositories and their files under
https://bitbucket.org/account/user/lorainelab/projects/IGB - Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers.
- Next, trigger the main branch pipeline. (See Canvas course module Building IGB for how to do this.)
- Check that files IGB-macos-universal-main.dmg, IGB-windows-amd64-main.exe, IGB-linux-amd64-main.sh, and main.jar got copied to the Downloads section of your fork.
If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are:
- You need to run the pipeline “custom: build-installers-for-dev ” on Bitbucket to create installers, rather than the “custom: manual-build” pipeline which creates the IGB jar file.
- Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available.
- Your user account does not have access to the installer private content repository. Make sure that you can see the files in the private repository when logged in to bitbucket.
- Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined.
- Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes.
- Double-check that your Bitbucket username is correct by selecting Settings > Personal Bitbucket settings > Account settings > Username.
Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review.
Reviewers should check that:
- This ticket has a comment with a link to the developer's fork
- The main branch installers are present in the fork's Downloads section
- When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present.
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IGBF-2404 Suggest improvements to pipelines on-boarding tickets using insights from RW and JW
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- Closed
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Show 2 more links (2 relates to)
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1762 [ 17852 ] |
| Rank | Ranked higher |
| Summary | On-boarding: Fork IGB team repository and set up bitbucket pipelines | On-boarding: Step Two - Fork IGB team repository and set up bitbucket pipelines |
| Summary | On-boarding: Step Two - Fork IGB team repository and set up bitbucket pipelines | On-boarding: Step Two - fork IGB team repository and set up bitbucket pipelines |
| Description |
Log in to bitbucket using your bitbucket user account that Dr. Loraine has added to the Loraine Lab team.
Review the IGB project repositories in the Loraine Lab account. Next, create a fork of the Integrated Genome Browser repository: * https://bitbucket.org/lorainelab/integrated-genome-browser Set up bitbucket pipelines following the instructions. Then set up bitbucket pipelines, following the instructions in |
Log in to bitbucket using your bitbucket user account that Dr. Loraine has added to the Loraine Lab team.
To check that your account got added to the team properly, review the IGB project repositories: https://bitbucket.org/account/user/lorainelab/projects/IGB Make sure you can see the private repositories. Next, create a fork of the Integrated Genome Browser repository: * https://bitbucket.org/lorainelab/integrated-genome-browser Set up bitbucket pipelines following the instructions in the private installer repository. Test that the pipeline is working by triggering the master branch pipeline. If you set things up properly, the master branch installers will be built and copied to the Downloads section of your fork. |
| Summary | On-boarding: Step Two - fork IGB team repository and set up bitbucket pipelines | On-boarding: Step 2 - fork IGB team repository and set up bitbucket pipelines |
| Description |
Log in to bitbucket using your bitbucket user account that Dr. Loraine has added to the Loraine Lab team.
To check that your account got added to the team properly, review the IGB project repositories: https://bitbucket.org/account/user/lorainelab/projects/IGB Make sure you can see the private repositories. Next, create a fork of the Integrated Genome Browser repository: * https://bitbucket.org/lorainelab/integrated-genome-browser Set up bitbucket pipelines following the instructions in the private installer repository. Test that the pipeline is working by triggering the master branch pipeline. If you set things up properly, the master branch installers will be built and copied to the Downloads section of your fork. |
Log in to bitbucket using your bitbucket user account that Dr. Loraine has added to the Loraine Lab team.
To check that your account got added to the team properly, review the IGB project repositories: https://bitbucket.org/account/user/lorainelab/projects/IGB Make sure you can see the private repositories. Next, create a fork of the Integrated Genome Browser repository: * https://bitbucket.org/lorainelab/integrated-genome-browser Set up bitbucket pipelines following the instructions in the private installer repository. Test that the pipeline is working by triggering the master branch pipeline. If you set things up properly, the master branch installers will be built and copied to the Downloads section of your fork. If you do not see the installers, then you need to work on the configuration. |
| Workflow | Loraine Lab Workflow [ 18486 ] | Fall 2019 Workflow Update [ 18977 ] |
| Workflow | Fall 2019 Workflow Update [ 18977 ] | Revised Fall 2019 Workflow Update [ 21097 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Fall 5 : 14 Oct to 25 Oct [ 76 ] | |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Ann Loraine [ aloraine ] |
Can you add a link to your fork? Philip Badzuh
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] | Philip Badzuh [ pbadzuh ] |
I am now a member of the team repo and have made a fork at https://bitbucket.org/pbadzuh/igb_pb_fork/src/master/
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
Above changed to https://bitbucket.org/pbadzuh/igb_pbdev/src/master/ to maximize build minutes by using "edu" email account to sign up.
Looks like pipelines may need to be reconfigured as the most recent build has failed. Philip Badzuh - please let me know if I need to make any changes to assist!
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
I believe I cancelled build #8 on my fork as it had already been successfully built before - I had reset a commit and didn't think the automatic repeat build was necessary.
I have since then rerun the build, just to make sure, and it builds successfully.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| 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 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| 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 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Sprint | Fall 5 : 14 Oct to 25 Oct [ 76 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov [ 76, 77 ] |
| 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 ] |
| 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 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Description |
Log in to bitbucket using your bitbucket user account that Dr. Loraine has added to the Loraine Lab team.
To check that your account got added to the team properly, review the IGB project repositories: https://bitbucket.org/account/user/lorainelab/projects/IGB Make sure you can see the private repositories. Next, create a fork of the Integrated Genome Browser repository: * https://bitbucket.org/lorainelab/integrated-genome-browser Set up bitbucket pipelines following the instructions in the private installer repository. Test that the pipeline is working by triggering the master branch pipeline. If you set things up properly, the master branch installers will be built and copied to the Downloads section of your fork. If you do not see the installers, then you need to work on the configuration. |
Log in to bitbucket using your bitbucket user account that Dr. Loraine has added to the Loraine Lab team.
To check that your account got added to the team properly, review the IGB project repositories: https://bitbucket.org/account/user/lorainelab/projects/IGB Make sure you can see the private repositories. Next, create a fork of the Integrated Genome Browser repository: * https://bitbucket.org/lorainelab/integrated-genome-browser Set up bitbucket pipelines following the instructions in the private installer repository. Test that the pipeline is working by triggering the master branch pipeline. If you set things up properly, the master branch installers will be built and copied to the Downloads section of your fork. If you do not see the installers, then you need to work on the configuration. |
| Sprint | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov [ 76, 77 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun [ 76, 77, 95 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Successful pipeline
https://bitbucket.org/Gchamma/integrated-genome-browser/addon/pipelines/home#!/results/3
[~aloraine]
Successful pipeline build
https://bitbucket.org/Rweidenh/integrated-genome-browser/addon/pipelines/home#!/results/4
[~aloraine]
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Please move to Closed.
cc: Jay Chamma and Logan Weidenhammer
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| 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 ] |
| Description |
Log in to bitbucket using your bitbucket user account that Dr. Loraine has added to the Loraine Lab team.
To check that your account got added to the team properly, review the IGB project repositories: https://bitbucket.org/account/user/lorainelab/projects/IGB Make sure you can see the private repositories. Next, create a fork of the Integrated Genome Browser repository: * https://bitbucket.org/lorainelab/integrated-genome-browser Set up bitbucket pipelines following the instructions in the private installer repository. Test that the pipeline is working by triggering the master branch pipeline. If you set things up properly, the master branch installers will be built and copied to the Downloads section of your fork. If you do not see the installers, then you need to work on the configuration. |
Review:
https://canvas.instructure.com/courses/1164217 Focus on the section titled "Building IGB". Follow the instructions for setting up Bitbucket pipelines. Once that is done, make sure you can build the IGB installers. Only members of the Loraine Lab Developers group in Bitbucket can do this. To build IGB installers: * Log in to bitbucket using your bitbucket user account that Dr. Loraine has added to the Loraine Lab team. * To check that your account got added to the team properly, review the IGB project repositories: https://bitbucket.org/account/user/lorainelab/projects/IGB * Make sure you can see the private repositories. * Trigger the master branch pipeline. * Check that the installers were copied to your Downloads section. If you do not see the installers, then you need to work on the configuration. |
| Description |
Review:
https://canvas.instructure.com/courses/1164217 Focus on the section titled "Building IGB". Follow the instructions for setting up Bitbucket pipelines. Once that is done, make sure you can build the IGB installers. Only members of the Loraine Lab Developers group in Bitbucket can do this. To build IGB installers: * Log in to bitbucket using your bitbucket user account that Dr. Loraine has added to the Loraine Lab team. * To check that your account got added to the team properly, review the IGB project repositories: https://bitbucket.org/account/user/lorainelab/projects/IGB * Make sure you can see the private repositories. * Trigger the master branch pipeline. * Check that the installers were copied to your Downloads section. If you do not see the installers, then you need to work on the configuration. |
Enroll in this free Canvas course:
https://canvas.instructure.com/courses/1164217 Read and study all the modules. Study the section titled "Building IGB". Follow the instructions for setting up Bitbucket pipelines. Once that is done, make sure you can build the IGB installers. Only members of the Loraine Lab Developers group in Bitbucket can do this. To build IGB installers: * Log in to bitbucket using your bitbucket user account that Dr. Loraine has added to the Loraine Lab team. * To check that your account got added to the team properly, review the IGB project repositories: https://bitbucket.org/account/user/lorainelab/projects/IGB * Make sure you can see the private repositories. * Trigger the master branch pipeline. * Check that the installers were copied to your Downloads section. If you do not see the installers, then you need to work on the configuration. |
| Description |
Enroll in this free Canvas course:
https://canvas.instructure.com/courses/1164217 Read and study all the modules. Study the section titled "Building IGB". Follow the instructions for setting up Bitbucket pipelines. Once that is done, make sure you can build the IGB installers. Only members of the Loraine Lab Developers group in Bitbucket can do this. To build IGB installers: * Log in to bitbucket using your bitbucket user account that Dr. Loraine has added to the Loraine Lab team. * To check that your account got added to the team properly, review the IGB project repositories: https://bitbucket.org/account/user/lorainelab/projects/IGB * Make sure you can see the private repositories. * Trigger the master branch pipeline. * Check that the installers were copied to your Downloads section. If you do not see the installers, then you need to work on the configuration. |
Enroll in this free Canvas course:
https://canvas.instructure.com/courses/1164217 Read and study Modules Study the section titled "Building IGB". Follow the instructions for setting up Bitbucket pipelines. Once that is done, make sure you can build the IGB installers. Only members of the Loraine Lab Developers group in Bitbucket can do this. To build IGB installers: * Log in to bitbucket using your bitbucket user account that Dr. Loraine has added to the Loraine Lab team. * To check that your account got added to the team properly, review the IGB project repositories: https://bitbucket.org/account/user/lorainelab/projects/IGB * Make sure you can see the private repositories. * Trigger the master branch pipeline. * Check that the installers were copied to your Downloads section. If you do not see the installers, then you need to work on the configuration. |
| Story Points | 0.5 | 3 |
| Description |
Enroll in this free Canvas course:
https://canvas.instructure.com/courses/1164217 Read and study Modules Study the section titled "Building IGB". Follow the instructions for setting up Bitbucket pipelines. Once that is done, make sure you can build the IGB installers. Only members of the Loraine Lab Developers group in Bitbucket can do this. To build IGB installers: * Log in to bitbucket using your bitbucket user account that Dr. Loraine has added to the Loraine Lab team. * To check that your account got added to the team properly, review the IGB project repositories: https://bitbucket.org/account/user/lorainelab/projects/IGB * Make sure you can see the private repositories. * Trigger the master branch pipeline. * Check that the installers were copied to your Downloads section. If you do not see the installers, then you need to work on the configuration. |
Enroll in this free Canvas course:
https://canvas.instructure.com/courses/1164217 Review Modules 1 through 4, focusing special attention to "Building IGB". Following the instructions, for the IGB repository and configure your fork to build the IGB installers for the main development branch. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your repository environment variable BB_AUTH_STRING is not properly configured. * Your repository |
| Summary | On-boarding: Step 2 - fork IGB team repository and set up bitbucket pipelines | On-boarding: Step 2 - fork IGB team repository and set up bitbucket pipelines to build installers |
| Description |
Enroll in this free Canvas course:
https://canvas.instructure.com/courses/1164217 Review Modules 1 through 4, focusing special attention to "Building IGB". Following the instructions, for the IGB repository and configure your fork to build the IGB installers for the main development branch. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your repository environment variable BB_AUTH_STRING is not properly configured. * Your repository |
Enroll in this free Canvas course:
https://canvas.instructure.com/courses/1164217 Review Modules 1 through 4, focusing special attention to "Building IGB". Following the instructions, for the IGB repository and configure your fork to build the IGB installers for the main development branch. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. |
| Description |
Enroll in this free Canvas course:
https://canvas.instructure.com/courses/1164217 Review Modules 1 through 4, focusing special attention to "Building IGB". Following the instructions, for the IGB repository and configure your fork to build the IGB installers for the main development branch. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. |
*Note*: Completing this on-boarding task will likely take 3 full days or more, depending on your experience level.
Enroll in this free Canvas course: https://canvas.instructure.com/courses/1164217 Review Modules 1 through 4, focusing special attention to "Building IGB". Following the instructions, for the IGB repository and configure your fork to build the IGB installers for the main development branch. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. |
| Description |
*Note*: Completing this on-boarding task will likely take 3 full days or more, depending on your experience level.
Enroll in this free Canvas course: https://canvas.instructure.com/courses/1164217 Review Modules 1 through 4, focusing special attention to "Building IGB". Following the instructions, for the IGB repository and configure your fork to build the IGB installers for the main development branch. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. |
*Note*: Completing this on-boarding task will likely take 3 full days or more, depending on your experience level. That is fine! Go slow and take your time.
Instructions: Enroll in this free Canvas course: https://canvas.instructure.com/courses/1164217 Review Modules 1 through 4, focusing special attention to "Building IGB". Following the instructions, for the IGB repository and configure your fork to build the IGB installers for the main development branch. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. |
| Description |
*Note*: Completing this on-boarding task will likely take 3 full days or more, depending on your experience level. That is fine! Go slow and take your time.
Instructions: Enroll in this free Canvas course: https://canvas.instructure.com/courses/1164217 Review Modules 1 through 4, focusing special attention to "Building IGB". Following the instructions, for the IGB repository and configure your fork to build the IGB installers for the main development branch. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. |
*Note*: Completing this on-boarding task will likely take 3 full days or more, depending on your experience level. That is fine! Go slow and take your time.
Instructions: Enroll in this free Canvas course: https://canvas.instructure.com/courses/1164217 Review Modules 1 through 4, focusing special attention to "Building IGB". Following the instructions, fork the IGB repository and configure your fork to build the IGB installers for the main development branch. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. |
| Description |
*Note*: Completing this on-boarding task will likely take 3 full days or more, depending on your experience level. That is fine! Go slow and take your time.
Instructions: Enroll in this free Canvas course: https://canvas.instructure.com/courses/1164217 Review Modules 1 through 4, focusing special attention to "Building IGB". Following the instructions, fork the IGB repository and configure your fork to build the IGB installers for the main development branch. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. |
*Note*: Completing this on-boarding task will likely take 3 full days or more, depending on your experience level. That is fine! Go slow and take your time.
Instructions: Enroll in this free Canvas course: https://canvas.instructure.com/courses/1164217 Review Modules 1 through 4, focusing special attention to "Building IGB". Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. |
| Description |
*Note*: Completing this on-boarding task will likely take 3 full days or more, depending on your experience level. That is fine! Go slow and take your time.
Instructions: Enroll in this free Canvas course: https://canvas.instructure.com/courses/1164217 Review Modules 1 through 4, focusing special attention to "Building IGB". Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. |
*Note*: Completing this on-boarding task will likely take 3 full days or more, depending on your experience level. That is fine! Go slow and take your time.
Instructions: Enroll in this free Canvas course: https://canvas.instructure.com/courses/1164217 Review Modules 1 through 4, focusing special attention to "Building IGB". Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that your master branch installers got built. |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Sprint | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun [ 76, 77, 95 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul [ 76, 77, 95, 98 ] |
| Assignee | Chirag Chandrahas Shetty [ chirag24 ] |
| Description |
*Note*: Completing this on-boarding task will likely take 3 full days or more, depending on your experience level. That is fine! Go slow and take your time.
Instructions: Enroll in this free Canvas course: https://canvas.instructure.com/courses/1164217 Review Modules 1 through 4, focusing special attention to "Building IGB". Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that your master branch installers got built. |
*Note*: Completing this on-boarding task will likely take 3 full days or more, depending on your experience level. That is fine! Go slow and take your time.
Instructions: Enroll in this free Canvas course: https://canvas.instructure.com/courses/1164217 Review Modules 1 through 4, focusing special attention to "Building IGB". Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Reviewing:
- This ticket has a comment with a link to the developer's fork - DONE
- The master branch installers are present in the fork's Downloads section - DONE
- When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. - DONE
Moving to Closed.
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| 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 ] |
| Assignee | Chirag Chandrahas Shetty [ chirag24 ] | Chester Dias [ cdias1 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul [ 76, 77, 95, 98 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul [ 76, 77, 95, 98, 99 ] |
| Rank | Ranked higher |
Fork link: https://bitbucket.org/chesterdias/integrated-genome-browser-chester-local/src
Pipeline Link: https://bitbucket.org/chesterdias/integrated-genome-browser-chester-local/addon/pipelines/home#!/results/3
Pipeline seems to run creating a jar in the download section.
[~aloraine], Philip Badzuh, Chirag Chandrahas Shetty, Jay Chamma
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Chester Dias [ cdias1 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
In reviewing:
- a personal fork has been made
- pipelines run successfully, and master branch installers are present
x - the latest commit message does not seem to include a jira issue link - it should be something like:
"IGBF-1764: Initial Bitbucket Pipelines configuration"
Moving back to to-do and assigning to Chester to amend commit message.
| Assignee | Philip Badzuh [ pbadzuh ] | Chester Dias [ cdias1 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
I am running macOS: Catalina V10.15.5
Had earlier install netbeans8. I had faced the below issues.
When we open/import a project, In the file open dialog box I noticed that folder names came blank or invisible by default,
Only when I clicked a folder in particular I was able to view folder name.
So in order to view any folder name, I had to navigate individually clicking on folder names
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Philip Badzuh
I have amended the name in the new repository. Please check everything again.
Fork: https://bitbucket.org/chesterdias/integrated-genome-browser/
| Assignee | Chester Dias [ cdias1 ] | Philip Badzuh [ pbadzuh ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Link | This issue is cloned by IGBF-2483 [ IGBF-2483 ] |
Great, everything looks good. Moving to Done, as there is nothing to merge.
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| 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 ] |
| Assignee | Philip Badzuh [ pbadzuh ] | Chester Dias [ cdias1 ] |
Testing results:
After following the instructions in the Canvas course:
- Created a personal fork
- The .jar file successfully appeared in the download section after running the pipeline
- master.exe and master.jar succesfully created (only after adding the INSTALL4J_LICENSE app password)
I have a few changes in mind that could be beneficial, [~aloraine]
First Change:
Change Settings to Repository Settings since that is the name of the repository settings in BitBucket.
From <https://canvas.instructure.com/courses/1164217/pages/set-up-bitbucket-pipelines?module_item_id=14594728>
Add the App password to your fork:
1. Go back to your fork
2. Click Settings
3. Choose Repository Variables
Second Change:
From <https://canvas.instructure.com/courses/1164217/pages/set-up-bitbucket-pipelines?module_item_id=14594728>
Change the text from:
Name it BB_AUTH_STRING - click the lock icon to keep it private!"
To:
"Name it BB_AUTH_STRING - check the 'Secured' option to keep it private!"
There is no lock icon to click on when creating a new repository variable, instead the user can check an option called "secured".
A lock appears on the right side of the variable after creation, which lets the user know that it's secured.
Third Change
Tell the reader to go to the IGB Installer Private Content repo in the Loraine Lab Repositories to access the three important app passwords (INSTALL4J_LICENSE, WIN_KEYSTORE_PASSWORD, MAC_KEYSTORE_PASSWOR).
There is a mention of them here:
From <https://canvas.instructure.com/courses/1164217/pages/set-up-bitbucket-pipelines?module_item_id=14594728>
To run pipelines which build IGB installers, your account needs access to some private assets available only to the core IGB team. Unfortunately, we can't distribute these assets publicly because of licensing restrictions.
However, the reader is not told how to access them, and since the IGB Installer Private Content repository is private, I don't see an issue with providing its name on the Canvas page.
Quick question: Who else besides future IGB developers will be reading this Canvas page?
Reply:
Canvas course is also for community members interested in modifying IGB or creating IGB Apps.
Changes made as recommended.
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Chester Dias [ cdias1 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Description |
*Note*: Completing this on-boarding task will likely take 3 full days or more, depending on your experience level. That is fine! Go slow and take your time.
Instructions: Enroll in this free Canvas course: https://canvas.instructure.com/courses/1164217 Review Modules 1 through 4, focusing special attention to "Building IGB". Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
*Note*: Completing this on-boarding task will likely take 3 full days or more, depending on your experience level. That is fine! Go slow and take your time.
Instructions: Enroll in this free Canvas course: https://canvas.instructure.com/courses/1164217 Carefully read modules 1 through 4. Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
| Description |
*Note*: Completing this on-boarding task will likely take 3 full days or more, depending on your experience level. That is fine! Go slow and take your time.
Instructions: Enroll in this free Canvas course: https://canvas.instructure.com/courses/1164217 Carefully read modules 1 through 4. Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
Carefully read modules 2, 3, and 4 of the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
| Story Points | 3 | 2 |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Sai Supreeth Segu [ ssegu ] |
Created fork and pipeline successfully
Pipeline link: https://bitbucket.org/supreeth27/integrated-genome-browser/addon/pipelines/home#!/results/3
Fork link: https://bitbucket.org/supreeth27/integrated-genome-browser/src/master/
cc: [~aloraine]
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Sprint | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul [ 76, 77, 95, 98, 99 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug [ 76, 77, 95, 98, 99, 101 ] |
Please un-assign the ticket to let people know it is available for review.
attn: Sai Supreeth Segu
| Assignee | Sai Supreeth Segu [ ssegu ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
Reviewed this ticket.
1) The ticket contains links to the developer's fork.
2) The master branch installers are present in the fork's Downloads section and when installed, IGB runs perfectly fine.
3) On checking the commit history on the fork, JIRA issue IGBF- hyperlinks are present
Moving this ticket to closed.
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| 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 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] | Sai Supreeth Segu [ ssegu ] |
| Assignee | Sai Supreeth Segu [ ssegu ] | Irvin Naylor [ inaylor ] |
| 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 ] |
| Assignee | Irvin Naylor [ inaylor ] |
| Description |
Carefully read modules 2, 3, and 4 of the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
Carefully read modules 2, 3, and 4 of the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section (they have extensions .exe, .dmg, and .sh) * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
| Description |
Carefully read modules 2, 3, and 4 of the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the master branch pipeline. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section (they have extensions .exe, .dmg, and .sh) * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
Carefully read modules 2, 3, and 4 of the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the *master branch pipeline*. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master-32bit.exe, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
Review criteria (see above) are met, but the master branch installers are not present in the fork's Downloads section.
Irvin Naylor - please review the Canvas module for information about how to build and test the master branch installers.
| Assignee | Irvin Naylor [ inaylor ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Sprint | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug [ 76, 77, 95, 98, 99, 101 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep [ 76, 77, 95, 98, 99, 101, 102 ] |
| Rank | Ranked higher |
| Sprint | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep [ 76, 77, 95, 98, 99, 101, 102 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep [ 76, 77, 95, 98, 99, 101, 102, 103 ] |
| Rank | Ranked higher |
Feedback we found from Canvas modules - set up bitbucket pipelines:
- When running pipeline for a branch, default pipeline should be reworded to default meaning default-IGB-* rather than literal 'default' one
- On Canvas, when the user is creating a new repo variable, BB-AUTH-STRING, they don't have a link to the private repo they should get access to upon completing the steps.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Irvin Naylor [ inaylor ] |
| Sprint | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep [ 76, 77, 95, 98, 99, 101, 102, 103 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep [ 76, 77, 95, 98, 99, 101, 102 ] |
| Description |
Carefully read modules 2, 3, and 4 of the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can see private IGB project repositories under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the *master branch pipeline*. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master-32bit.exe, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
Carefully read modules 2, 3, and 4 of the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can open and see private (as denoted by a "padlock" icon) IGB project repositories and their files under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the *master branch pipeline*. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master-32bit.exe, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * You need to run the branch pipeline “Branches - IGBF*” on Bitbucket to create installers, rather than the “default” pipeline which creates the IGB jar file. * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the files in the private repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
| Description |
Carefully read modules 2, 3, and 4 of the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can open and see private (as denoted by a "padlock" icon) IGB project repositories and their files under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the *master branch pipeline*. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master-32bit.exe, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * You need to run the branch pipeline “Branches - IGBF*” on Bitbucket to create installers, rather than the “default” pipeline which creates the IGB jar file. * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the files in the private repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
Carefully read modules 2, 3, and 4 of the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can open and see private (as denoted by a "padlock" icon) IGB project repositories and their files under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the *master branch pipeline*. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master-32bit.exe, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * You need to run the branch pipeline “branches: IGBF-* ” on Bitbucket to create installers, rather than the “default” pipeline which creates the IGB jar file. * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the files in the private repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
Instructions are revised 10/01.
| Assignee | Irvin Naylor [ inaylor ] |
On-boarding Step 2 revision comments:
- “Carefully read modules 2, 3, and 4 of the online course..”
I personally think they should only read Modules 2 and 3 since those chiefly involve the pipelines and setting up their fork. Since the next step involves the workflow (Module 4), it would make sense for only these two modules to be active.
-I think it should be a bit more clear if they should do the instructions in modules 2 and 3 before building the IGB installers. I could see how someone could get turned around if they read through the to build IGB installers section first.
-Overall, the general flow of the steps is much clearer to understand in regards to everything else
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Description |
Carefully read modules 2, 3, and 4 of the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can open and see private (as denoted by a "padlock" icon) IGB project repositories and their files under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the *master branch pipeline*. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master-32bit.exe, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * You need to run the branch pipeline “branches: IGBF-* ” on Bitbucket to create installers, rather than the “default” pipeline which creates the IGB jar file. * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the files in the private repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
Read modules 2 and 3 the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can open and see private (as denoted by a "padlock" icon) IGB project repositories and their files under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the *master branch pipeline*. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master-32bit.exe, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * You need to run the branch pipeline “branches: IGBF-* ” on Bitbucket to create installers, rather than the “default” pipeline which creates the IGB jar file. * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the files in the private repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| 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 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Assignee | Irvin Naylor [ inaylor ] | Omkar Marne [ omarne ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep [ 76, 77, 95, 98, 99, 101, 102 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19 [ 76, 77, 95, 98, 99, 101, 102, 114 ] |
My account has been added to the Developers group and I can access the https://bitbucket.org/account/user/lorainelab/projects/IGB
I am able to run the IGB on my local machine now.
Bitbucket pipelines have been successfully set up. All the repository variables have been added. I can see master.dmg, master-32bit.exe, master.exe, master.sh, and master.jar in the downloads folder and can see the commits history.
Link to the developer's fork. - https://bitbucket.org/account/user/lorainelab/projects/IGB
Link to the downloads folder - https://bitbucket.org/omarne/integrated-genome-browser/downloads/
Link to check the commit history - https://bitbucket.org/omarne/integrated-genome-browser/commits/ ; IGBF hyperlinks are present.
Link to my fork - https://bitbucket.org/omarne/integrated-genome-browser/src/master/
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Omkar Marne [ omarne ] |
| Sprint | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19 [ 76, 77, 95, 98, 99, 101, 102, 114 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5 [ 76, 77, 95, 98, 99, 101, 102, 114, 115 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| 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 ] |
Omkar Marne Review:
- Link to fork works as expected
- Master branch installers are indeed present in the downloads section.
- Jira hyperlinks work as expected on the commit section of the fork.
Everything looks good. Moving issue to closed.
| Assignee | Jay Ostwal [ jayostwal ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Sprint | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5 [ 76, 77, 95, 98, 99, 101, 102, 114, 115 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 4 2021 May 3 - May 14 [ 76, 77, 95, 98, 99, 101, 102, 114, 115, 120 ] |
Created fork successfully and all the bucket pipelines and installers have been installed and set up. I am attaching the links as below :
Link to my fork : https://bitbucket.org/jayostwal/integrated-genome-browser/src/master/
Link to the downloads folder : https://bitbucket.org/jayostwal/integrated-genome-browser/downloads/
Link to pipeline results : https://bitbucket.org/jayostwal/integrated-genome-browser/addon/pipelines/home#!/results/13
Link to commits : https://bitbucket.org/jayostwal/integrated-genome-browser/commits/
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Jay Ostwal [ jayostwal ] | Irvin Naylor [ inaylor ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Jay Ostwal review:
- Jay's comment does include a link to his link.
- Master Branch installers do show up.
- IGB Commit history does show up correctly and hyperlinks work as intended.
Everything checks out, moving to closed.
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| 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 ] |
| Assignee | Irvin Naylor [ inaylor ] | Jay Ostwal [ jayostwal ] |
| Assignee | Jay Ostwal [ jayostwal ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Sprint | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 4 2021 May 3 - May 14 [ 76, 77, 95, 98, 99, 101, 102, 114, 115, 120 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 4 2021 May 3 - May 14, Summer 1 2023 May 15 [ 76, 77, 95, 98, 99, 101, 102, 114, 115, 120, 170 ] |
| Assignee | Kaushik Gopu [ kgopu ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 4 2021 May 3 - May 14, Summer 1 2023 May 15 [ 76, 77, 95, 98, 99, 101, 102, 114, 115, 120, 170 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 4 2021 May 3 - May 14, Summer 1 2023 May 15, Summer 2 2023 May 29 [ 76, 77, 95, 98, 99, 101, 102, 114, 115, 120, 170, 171 ] |
| Rank | Ranked higher |
| Description |
Read modules 2 and 3 the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can open and see private (as denoted by a "padlock" icon) IGB project repositories and their files under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the *master branch pipeline*. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master-32bit.exe, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * You need to run the branch pipeline “branches: IGBF-* ” on Bitbucket to create installers, rather than the “default” pipeline which creates the IGB jar file. * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the files in the private repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
Read modules 2 and 3 the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can open and see private (as denoted by a "padlock" icon) IGB project repositories and their files under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the *master branch pipeline*. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master-32bit.exe, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * You need to run the branch pipeline “branches: IGBF-* ” on Bitbucket to create installers, rather than the “default” pipeline which creates the IGB jar file. * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the files in the private repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. * Double-check that your Bitbucket username is correct in BB_AUTH_STRING by selecting Settings > Personal Bitbucket settings > Account settings > Username. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
pipeline setup working fine, forking done, project setup in local done.
Link to the downloads folder->https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/downloads/
Link to the developer's fork->https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/src/master/
Link to check the commit history->https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/commits/
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Description |
Read modules 2 and 3 the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can open and see private (as denoted by a "padlock" icon) IGB project repositories and their files under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the *master branch pipeline*. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master-32bit.exe, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * You need to run the branch pipeline “branches: IGBF-* ” on Bitbucket to create installers, rather than the “default” pipeline which creates the IGB jar file. * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the files in the private repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. * Double-check that your Bitbucket username is correct in BB_AUTH_STRING by selecting Settings > Personal Bitbucket settings > Account settings > Username. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
Read modules 2 and 3 the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can open and see private (as denoted by a "padlock" icon) IGB project repositories and their files under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the *master branch pipeline*. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master-32bit.exe, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * You need to run the branch pipeline “branches: IGBF-* ” on Bitbucket to create installers, rather than the “default” pipeline which creates the IGB jar file. * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the files in the private repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. * Double-check that your Bitbucket username is correct by selecting Settings > Personal Bitbucket settings > Account settings > Username. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
| Assignee | Kaushik Gopu [ kgopu ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| 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 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Sprint | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 4 2021 May 3 - May 14, Summer 1 2023 May 15, Summer 2 2023 May 29 [ 76, 77, 95, 98, 99, 101, 102, 114, 115, 120, 170, 171 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 4 2021 May 3 - May 14, Summer 1 2023 May 15, Summer 2 2023 May 29, Fall 3 2023 Oct 2 [ 76, 77, 95, 98, 99, 101, 102, 114, 115, 120, 170, 171, 179 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Pipeline setup is done and working fine, except for the notarization part for MAC OS as the tool (altool) used to notarize is deprecated, I have informed this to Nowlan Freese and created a ticket for the same https://jira.bioviz.org/browse/IGBF-3468. Apart from that everything else works fine.
Link to my fork: https://bitbucket.org/jaya-sravani/integrated-genome-browser/src/main-JDK8/
Link to commit history: https://bitbucket.org/jaya-sravani/integrated-genome-browser/commits/
Link to downloads folder: https://bitbucket.org/jaya-sravani/integrated-genome-browser/downloads/
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Ann Loraine [ aloraine ] |
Reviewing:
- Links back to Jira tickets from the fork are working as expected
- Downloads folder contains installers for Mac, Windows, and Linux as expected
- Downloaded and ran the installer; observed the expected warning from my Mac due to lack of notarization. This is the expected behavior.
Moving to Done.
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| 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 ] |
| Assignee | Ann Loraine [ aloraine ] | Jaya Sravani Sirigineedi [ jsirigin ] |
| Sprint | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 4 2021 May 3 - May 14, Summer 1 2023 May 15, Summer 2 2023 May 29, Fall 3 2023 Oct 2 [ 76, 77, 95, 98, 99, 101, 102, 114, 115, 120, 170, 171, 179 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 4 2021 May 3 - May 14, Summer 1 2023 May 15, Summer 2 2023 May 29, Fall 3 2023 Oct 2, Spring 5 [ 76, 77, 95, 98, 99, 101, 102, 114, 115, 120, 170, 171, 179, 189 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] | Dylan Marrotte [ dmarrott ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Since Dylan Marrotte is going to be doing data analysis rather than IGB software development, I think it would be better for you to do tasks from the "learn the basics - data analysis" epic.
Un-assigning and moving back to "to-do"
Sorry for the confusion!
| Status | In Progress [ 3 ] | 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 ] |
| 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 ] |
| Assignee | Dylan Marrotte [ dmarrott ] |
| Sprint | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 4 2021 May 3 - May 14, Summer 1 2023 May 15, Summer 2 2023 May 29, Fall 3 2023 Oct 2, Spring 5 [ 76, 77, 95, 98, 99, 101, 102, 114, 115, 120, 170, 171, 179, 189 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 4 2021 May 3 - May 14, Summer 1 2023 May 15, Summer 2 2023 May 29, Fall 3 2023 Oct 2, Spring 5, Fall 4 [ 76, 77, 95, 98, 99, 101, 102, 114, 115, 120, 170, 171, 179, 189, 205 ] |
| Assignee | Udaya Chinta [ uchinta ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 4 2021 May 3 - May 14, Summer 1 2023 May 15, Summer 2 2023 May 29, Fall 3 2023 Oct 2, Spring 5, Fall 4 [ 76, 77, 95, 98, 99, 101, 102, 114, 115, 120, 170, 171, 179, 189, 205 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 4 2021 May 3 - May 14, Summer 1 2023 May 15, Summer 2 2023 May 29, Fall 3 2023 Oct 2, Spring 5, Fall 4, Fall 5 [ 76, 77, 95, 98, 99, 101, 102, 114, 115, 120, 170, 171, 179, 189, 205, 206 ] |
| Rank | Ranked higher |
I successfully setup the bitbucket pipeline as suggested in the documentation.
The documentation suggests to run the default pipeline but the default pipeline is not in use, instead custom manual build pipeline is being used. This needs to be updated in the documentation.
I ran the master pipeline and now the download folder contains the installers.
Below are the links
Link for fork: https://bitbucket.org/lorainelab_udaya/integrated-genome-browser/src/main/
Link for downloads folder: https://bitbucket.org/lorainelab_udaya/integrated-genome-browser/downloads/
Link for commit history: https://bitbucket.org/lorainelab_udaya/integrated-genome-browser/commits/branch/main
Since I am using windows, I downloaded the master.exe and successfully ran the application in my local.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Udaya Chinta [ uchinta ] |
Fork is created and is visible. But I see pipelines aren't enabled, she is getting a warning saying that the pipelines aren't enabled for the repository when trying to run the pipeline, assigning back to Udaya Chinta
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] | Udaya Chinta [ uchinta ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
I did not login to bitbucket initially, so I got an issue that you do not have write access to run pipelines. After logging in I faced the same issue for few minutes but after sometime I am able to run the pipelines, not sure why I got the issue initially.
Ran the main branch as suggested by Jaya Sravani Sirigineedi
Providing the link for the downloads folder: https://bitbucket.org/lorainelab_udaya/integrated-genome-browser/downloads/
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Udaya Chinta [ uchinta ] | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Review: Fork is created, installers are present and the commit history has Jira links. Ran the main mac installer in my machine, working as expected. Moving the ticket to done.
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| 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 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] | Udaya Chinta [ uchinta ] |
| Description |
Read modules 2 and 3 the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can open and see private (as denoted by a "padlock" icon) IGB project repositories and their files under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the *master branch pipeline*. (See Canvas course module *Building IGB* for how to do this.) * Check that files master.dmg, master-32bit.exe, master.exe, master.sh, and master.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * You need to run the branch pipeline “branches: IGBF-* ” on Bitbucket to create installers, rather than the “default” pipeline which creates the IGB jar file. * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the files in the private repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. * Double-check that your Bitbucket username is correct by selecting Settings > Personal Bitbucket settings > Account settings > Username. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The master branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
Read modules 2 and 3 the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can open and see private (as denoted by a "padlock" icon) IGB project repositories and their files under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the *main branch pipeline*. (See Canvas course module *Building IGB* for how to do this.) * Check that files IGB-macos-universal-main.dmg, IGB-windows-amd64-main.exe, IGB-linux-amd64-main.sh, and main.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * You need to run the branch pipeline “branches: IGBF-* ” on Bitbucket to create installers, rather than the “default” pipeline which creates the IGB jar file. * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the files in the private repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. * Double-check that your Bitbucket username is correct by selecting Settings > Personal Bitbucket settings > Account settings > Username. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The main branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
| Sprint | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 4 2021 May 3 - May 14, Summer 1 2023 May 15, Summer 2 2023 May 29, Fall 3 2023 Oct 2, Spring 5, Fall 4, Fall 5 [ 76, 77, 95, 98, 99, 101, 102, 114, 115, 120, 170, 171, 179, 189, 205, 206 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 4 2021 May 3 - May 14, Summer 1 2023 May 15, Summer 2 2023 May 29, Fall 3 2023 Oct 2, Spring 5, Fall 4, Fall 5, Fall 6 [ 76, 77, 95, 98, 99, 101, 102, 114, 115, 120, 170, 171, 179, 189, 205, 206, 207 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Assignee | Udaya Chinta [ uchinta ] |
| Rank | Ranked higher |
| Assignee | saideepthi jagarapu [ sjagarap ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Done with bitbucket pipeline setup following the module 3 of IGB canvas course documentation.
Have run the main branch pipeline using custom: manual-build which is successful and able to see installers in downloads folder
Repository fork link: https://bitbucket.org/lorainelab-deepthi/integrated-genome-browser/src/main/
Fork's Downloads section: https://bitbucket.org/lorainelab-deepthi/integrated-genome-browser/downloads/
Commit history on fork: https://bitbucket.org/lorainelab-deepthi/integrated-genome-browser/commits/branch/main
| Description |
Read modules 2 and 3 the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can open and see private (as denoted by a "padlock" icon) IGB project repositories and their files under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the *main branch pipeline*. (See Canvas course module *Building IGB* for how to do this.) * Check that files IGB-macos-universal-main.dmg, IGB-windows-amd64-main.exe, IGB-linux-amd64-main.sh, and main.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * You need to run the branch pipeline “branches: IGBF-* ” on Bitbucket to create installers, rather than the “default” pipeline which creates the IGB jar file. * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the files in the private repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. * Double-check that your Bitbucket username is correct by selecting Settings > Personal Bitbucket settings > Account settings > Username. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The main branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
Read modules 2 and 3 the on-line course "Open source programming with IGB."
Following the instructions, fork the IGB repository and configure your fork to build IGB platform-specific installers. To build IGB installers: * Log in to bitbucket using your bitbucket user account. * Check your account has been added to the Developers group by confirming that you can open and see private (as denoted by a "padlock" icon) IGB project repositories and their files under https://bitbucket.org/account/user/lorainelab/projects/IGB * Look for the installers private content repository. Follow the instructions there to create repository variables required to build installers. * Next, trigger the *main branch pipeline*. (See Canvas course module *Building IGB* for how to do this.) * Check that files IGB-macos-universal-main.dmg, IGB-windows-amd64-main.exe, IGB-linux-amd64-main.sh, and main.jar got copied to the Downloads section of your fork. If you do not see the installers, click the Pipelines button to review any error messages. The main problems people have when using pipelines are: * You need to run the pipeline “custom: build-installers-for-dev ” on Bitbucket to create installers, rather than the “custom: manual-build” pipeline which creates the IGB jar file. * Something has gone wrong with the Loraine Lab maven repository which hosts dependencies (jar files) needed for building IGB. Check that https://nexus.bioviz.org is available. * Your user account does not have access to the installer private content repository. Make sure that you can see the files in the private repository when logged in to bitbucket. * Your repository environment variables are not configured properly. Review the installer private contents repository again to make sure all repository environment variables are properly defined. * Your account has run out of Bitbucket pipeline minutes. Create a new bitbucket account using an "edu" domain to get more minutes. * Double-check that your Bitbucket username is correct by selecting Settings > Personal Bitbucket settings > Account settings > Username. Finally, add a new comment with a link to your fork and move this ticket to Needs First Level Review. Reviewers should check that: * This ticket has a comment with a link to the developer's fork * The main branch installers are present in the fork's Downloads section * When you view the commit history on the developer's fork, Jira IGBF issue hyperlinks are present. |
| Sprint | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 4 2021 May 3 - May 14, Summer 1 2023 May 15, Summer 2 2023 May 29, Fall 3 2023 Oct 2, Spring 5, Fall 4, Fall 5, Fall 6 [ 76, 77, 95, 98, 99, 101, 102, 114, 115, 120, 170, 171, 179, 189, 205, 206, 207 ] | Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Spring 9 : 25 May to 8 Jun, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 4 2021 May 3 - May 14, Summer 1 2023 May 15, Summer 2 2023 May 29, Fall 3 2023 Oct 2, Spring 5, Fall 4, Fall 5, Fall 6, Fall 7 [ 76, 77, 95, 98, 99, 101, 102, 114, 115, 120, 170, 171, 179, 189, 205, 206, 207, 208 ] |
| Rank | Ranked higher |
was not able open the dmg file from download section saying cannot open the software as it is malicious, followed this canvas course module and resolved https://canvas.instructure.com/courses/1164217/pages/how-to-notarize-installers-for-macos?module_item_id=42905992
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Thank you saideepthi jagarapu for the above comment. As you noted, this is an expected behavior on an Apple computer with "factory default" security settings.
saideepthi jagarapu: Currently this issue is assigned to you. I'm not sure what you want to do with this issue, but I'm guessing you want somebody else to review it. This is confusing because our convention is that if an issue is assigned to a person, then we assume that particular person is either working on it or is planning to work on it later, and does not need anybody else to do anything for it. So, if you forget to un-assign yourself from an issue, it will sit in "needs first level review" for a long time, blocking progress.
| Assignee | saideepthi jagarapu [ sjagarap ] |
Sorry Ann Loraine for the confusion caused. It was my mistake to leave the issue assigned to myself, and I’ll be more mindful to un-assign myself in the future to avoid blocking progress.
| Assignee | Udaya Chinta [ uchinta ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Review:
- The ticket has comment with a link to the developer's fork.
- The main branch installers are present in the download section.
- IGBF issue hyperlinks are present in commit history.
Moving the ticket to done.
| Status | First Level Review in Progress [ 10301 ] | 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 ] |
| 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 ] |
| Assignee | Udaya Chinta [ uchinta ] | saideepthi jagarapu [ sjagarap ] |
I'm not listed as a member on bitbucket/lorainelab and can't see the private repos