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  1. IGB
  2. IGBF-1764

On-boarding: Step 2 - fork IGB team repository and set up bitbucket pipelines to build installers

    Details

    • Type: Task
    • Status: Closed (View Workflow)
    • Priority: Blocker
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
    • Story Points:
      2
    • 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

      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.

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            Hide
            inaylor Irvin Naylor (Inactive) added a comment -

            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.

            Show
            inaylor Irvin Naylor (Inactive) added a comment - 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.
            Hide
            kgopu Kaushik Gopu added a comment -

            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/

            Show
            kgopu Kaushik Gopu added a comment - 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/
            Hide
            jsirigin Jaya Sravani Sirigineedi added a comment -

            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/

            Show
            jsirigin Jaya Sravani Sirigineedi added a comment - 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/
            Hide
            ann.loraine Ann Loraine added a comment -

            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.

            Show
            ann.loraine Ann Loraine added a comment - 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.
            Hide
            ann.loraine Ann Loraine added a comment -

            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!

            Show
            ann.loraine Ann Loraine added a comment - 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!

              People

              • Assignee:
                Unassigned
                Reporter:
                ann.loraine Ann Loraine
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                Watchers:
                12 Start watching this issue

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                • Created:
                  Updated:
                  Resolved: