Feedback:

Overall, this new version of the module is very straightforward and easy to follow. I was able to easily put myself in the shoes of someone new and easily walk through all seven steps. The only thing I might clarify is in step 7, telling them an indication of where the IGB toolbar is for the camera could be helpful especially if this might be their first time ever using IGB.

IGB screenshot attached:

Potential bug in IGB 9.1.4:
At the point where the user has loaded the data and is going to configure the graph tracks, selecting "select all" in the graph menu as the video describes does not seem to do anything. It worked before when I did it the first time, but now on subsequent tries, it doesn't. I've reinstalled 9.1.4 to make sure but it is still persisting. I just wanted to let you know and ask if there is any specific protocol on reporting bugs. The screenshot is of the next closest step before the graph track step, as a result.

Irvin Naylor
Noted your comment on step 7 and will add that to the improvements.

I just went through the steps and the "select all" worked fine.
Then I tried it again after reading your comment, you're right it doesn't work after that.
Have you tried resetting the preferences? Reinstalling IGB will keep your preferences from any previous installs.
To do this go to File > Preferences > Other Options > Reset Preferences to Defaults (at the bottom)
Or you can click the gear icon and select the reset preferences button at the bottom.

It started working again for me after I reset the preferences.
Good luck!

Logan Weidenhammer
Thanks for the suggestion! I reset the preferences but it looks like it's still there on my end. I've tried a few different read alignment combinations but I'm not sure what it could be. I'll keep fiddling around with it and see if I can find anything.

[~aloraine]

Dr. Loraine, you were totally right! I was putting reads instead of graphs, my bad. I've changed the screenshot to be in line with what the video was looking like at the end. In general, it looks like this step 0 is completely smooth and straightforward otherwise.

I'm not sure if the select all potential bug isn't actually a bug at all, in this case!

Moving to closed. Thank you for the feedback!

Feedback for Omkar Marne:

• Please note: You should un-assign the ticket when you move it to Needs First Level Review. Otherwise, no-one will review it because it looks like someone has already picked it up but is not working on reviewing it yet. Please ask Sai Supreeth Segu or Irvin Naylor for details.
• Please re-read the above instructions carefully. You need to enroll in the Canvas class but it appears this has not been done. (I could not find your name in the list of enrolled students.)
• The image attached does not match the end of the video. Kindly re-read the documentation for IGB to understand the difference between an annotation data type and a graph data type. Then watch the video again, following along as closely as you can.
• Please do not proceed to the next on-boarding ticket until the above has been completed.

My apologies. I went through the course without enrolling. Please check if my name in the list now.

I have uploaded the corrected image. I was able to do 'SELECT ALL' and change the X and Y axis for the coverage graphs.

Omkar Marne has enrolled in the class but image is not same as the final image in the video. Please go through the youtube link and follow each step to replicate final image.

IGB updated image

Please check the corrected IGB image.

Sai Supreeth Segu Please check the corrected IGB image and let me know if its wrong.

Omkar Marne Screenshot looks good to me. Moving the ticket to pull request

Thank you Sai Supreeth Segu

Day - 1: Enrolled in the canvas course and completed the first module. Installed IGB on my local machine and completed the steps mentioned in the video and the ticket, attached the required screenshot below.

Gone through the provided IGB documentation as well but these two links doesn't have any content in them. https://wiki.bioviz.org/confluence/display/ITD/IGB+Release+Documentation
https://wiki.bioviz.org/confluence/display/igbdevelopers/Home

UPDATE from Nowlan - Links are updated in the ticket description to:
https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first
https://wiki.bioviz.org/confluence/display/igbdevelopers/Developing+Integrated+Genome+Browser

Day - 2:
Completed the documentation regarding testing and started the developer's documentation. Created a bitbucket account and tried to fix an issue that occurred while setting up SSH.

When you move an issue to "needs review" or "needs testing" please do not assign it to a specific person, unless only that one specific person can review it, or if that person has asked for you to assign it to them. In this case, pretty much anybody on the team can review this particular issue, so you should leave it unassigned. I am usually the person with the biggest workload, so if at all possible you try not to assign things to me, because if you do, you might have to a wait a few days for me to get to it, which could slow you down

Sure, [~aloraine]. Actually, I didn't assign it, after I unassigned myself it got assigned to you directly I guess. I will make sure to check that from now on.

Review:

• The image has graphs loaded and configured to the same scale as each other
• Jaya Sravani Sirigineedi has enrolled in the class

Moving to done!

*Day1:

• Enrolled in canvas course and completed the module 1.
• Installed IGB and completed the steps mentioned in the youtube video. Attaching the screenshot for verification.
  
• Attaching the another screenshot where I have explored reads, annotations and graphs tabs.
  
  I have gone through the below documentations
• https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first
• https://wiki.bioviz.org/confluence/display/igbdevelopers/Developing+Integrated+Genome+Browser

Below are the doubts and I got them clarified from Professor Loraine and Dr Freese:

• What is the source for BAM file?
• Dont we have a feature to delete all tracks at a time in data management table?

Day 2:
I created an account in Bitbucket, forked the igb repository, and added an SSH key. I then tried to set up the local environment by cloning the Bitbucket repository, but it threw an error showing:
kex_exchange_identification: read: Software caused connection abort
banner exchange: Connection to 104.192.142.26 port 22: Software caused connection abort.
I resolved the above error. After resolving it, I received the following message:
authenticated via ssh key.
Now I am getting another error that I need to resolve.

The ticket is in the "needs review" column but the most recent comment added by Udaya Chinta indicates more work is needed to resolve a new error. So I am returning this to "To-Do" because more work needs to be done, according to comments added thus far.

Day 3: I am able to clone the code using https url and installed azul jdk 21. Maven build is successful on local machine.
Attaching the screenshot

Review:

• The image uploaded has the same graphs loaded and the scales also match the video.
• Udaya Chinta is enrolled in the Canvas course.

Moving the ticket to done.