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
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.
Attachments
Issue Links
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- Pull Request Submitted
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- is blocked by
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- To-Do
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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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Activity
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!
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.
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
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/
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.
I'm not listed as a member on bitbucket/lorainelab and can't see the private repos