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!

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.

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/

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/

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.

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/

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.

Link to my fork - https://bitbucket.org/omarne/integrated-genome-browser/src/master/

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.

I am able to run the IGB on my local machine now.

My account has been added to the Developers group and I can access the https://bitbucket.org/account/user/lorainelab/projects/IGB

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

Instructions are revised 10/01.

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.

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.

Pipeline: https://bitbucket.org/Inaylor01/integrated-genome-browser/addon/pipelines/home#!/results/2
Fork: https://bitbucket.org/Inaylor01/integrated-genome-browser/src/master/

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.

Please un-assign the ticket to let people know it is available for review.
attn: Sai Supreeth Segu

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]

Changes made as recommended.

Reply:

Canvas course is also for community members interested in modifying IGB or creating IGB Apps.

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?

Great, everything looks good. Moving to Done, as there is nothing to merge.

Philip Badzuh
I have amended the name in the new repository. Please check everything again.
Fork: https://bitbucket.org/chesterdias/integrated-genome-browser/

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

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.

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

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.

Fork link: https://bitbucket.org/chirag06/integrated-genome-browser/src/master/
pipeline link: https://bitbucket.org/chirag06/integrated-genome-browser/addon/pipelines/home#!/results/7
[~aloraine]

Please move to Closed.

cc: Jay Chamma and Logan Weidenhammer

Successful pipeline build
https://bitbucket.org/Rweidenh/integrated-genome-browser/addon/pipelines/home#!/results/4
[~aloraine]

Successful pipeline
https://bitbucket.org/Gchamma/integrated-genome-browser/addon/pipelines/home#!/results/3
[~aloraine]

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.

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!

I am now a member of the team repo and have made a fork at https://bitbucket.org/pbadzuh/igb_pb_fork/src/master/

Can you add a link to your fork? Philip Badzuh

I'm not listed as a member on bitbucket/lorainelab and can't see the private repos