Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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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:None
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Story Points:3
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Epic Link:
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Sprint:Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 3 2021 Apr 19 - Apr 30, Summer 1 2023 May 15, Fall 3 2023 Oct 2, Fall 4, Fall 5
Description
Welcome to your first on-boarding task for the IGB core development team!
We are super excited you have joined us! We hope you will enjoy your time with us and will make big contributions to the code base and the IGB community.
For the next steps, please do the following tasks to get familiar with IGB and how it is used.
Note that this issue has 3 story points.
A "story point" is an estimate for how long a task ought to take. One day is roughly equal to one story point.
This means you should expect to spend about three working days on this "on-boarding" task. Take your time on this task and explore the IGB interface to better understand how it works.
Reading:
IGB on-line canvas course:
- Enroll in https://canvas.instructure.com/courses/1164217
- In Module I of the course, read: IGB Background and Intro to IGB Data Visualization
IGB documentation:
- Visit the IGB user's guide and get familiar with all the contents: https://wiki.bioviz.org/confluence/display/igbman/Home
- Visit the IGB Release Documentation guide, which we use for testing new released. Get familiar with the contents: https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first
- Visit the IGB Developers guide and get familiar with the contents: https://wiki.bioviz.org/confluence/display/igbdevelopers/Developing+Integrated+Genome+Browser
Get started using IGB:
- Download and install the current release of IGB onto your computer from https://bioviz.org/
- Click the “install IGB” button in the top right. (The appropriate version for your operating system should be supplied for you.)
- Click the button to download IGB for your computer
- Run the downloaded file
- Follow the instructions in the setup wizard.
- Open and run the Integrated Genome Browser software.
- The IGB Quickstart webpage will open automatically in your web browser.
- IGB may take several seconds to launch.
- Using IGB, follow along and copy the actions shown in this video: https://www.youtube.com/watch?v=LjPNT1k9cqk
- Re-create the scene shown at the very end of the video.
- Then use the camera icon button in the IGB toolbar at the top, or go to File > Save Image to take a picture of IGB showing the scene at the end of the video;
- Upload that image here as an attachment (you can use the plus icon to the right of Attachments).
- Move the ticket to Needs 1st Level Review by clicking the Workflow dropdown button at the top (under the ticket name), and select Request Review. You could also drag the ticket over to the right one space from the Agile board > IGB > Work view.
- Since this might be the first ticket you do, and it needs to be completed before you move on to On-Boarding: Step 1 (Step 0 is a blocker for Step 1): Reach out to another developer here to review your ticket with you before you move on.
Reviewers:
- Watch https://www.youtube.com/watch?v=LjPNT1k9cqk
- Confirm that the assignee has uploaded an image with graphs loaded and configured to the same scale as each other, as shown in the video
- Confirm that the assignee has enrolled in the class. To do this select the People tab and look for the student’s name in the list.
Attachments
Issue Links
- blocks
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1762 [ 17852 ] |
| Summary | CLONE - On-Boarding: Step 0 - Module 1 of IGB course & running IGB | On-Boarding: Step 0 - Module 1 of IGB course & running IGB |
| Description |
Welcome to your first on-boarding task for the IGB core development team!
We are super excited you have joined us! We hope you will enjoy your time with us and will make big contributions to the code base and the IGB community. For this on-boarding task, please do the following: # Go to https://canvas.instructure.com and make a free account. # Log in and enroll in https://canvas.instructure.com/courses/1164217 # In Module I of the course, read: *IGB Background* and *Intro to IGB Data Visualization* # Download and install the current release of IGB onto your computer. # Using IGB, copy the actions shown in this IGB video: https://www.youtube.com/watch?v=LjPNT1k9cqk # Re-create the scene shown at the very end of the video. # Use the camera button in the IGB toolbar to take a picture of IGB showing the scene at the end of the video; upload it here Reviewers: * Watch https://www.youtube.com/watch?v=LjPNT1k9cqk * Confirm that the assignee has uploaded an image with graphs loaded and configured to the same scale as each other, as shown in the video * Confirm that the assignee has enrolled in the class. |
Welcome to your first on-boarding task for the IGB core development team!
We are super excited you have joined us! We hope you will enjoy your time with us and will make big contributions to the code base and the IGB community. For the next steps, please do the following: # Go to https://canvas.instructure.com and make a free account. # Log in and enroll in https://canvas.instructure.com/courses/1164217 # In Module I of the course, read: *IGB Background* and *Intro to IGB Data Visualization* # Download and install the current release of IGB onto your computer. # Using IGB, copy the actions shown in this IGB video: https://www.youtube.com/watch?v=LjPNT1k9cqk # Re-create the scene shown at the very end of the video. # Use the camera button in the IGB toolbar to take a picture of IGB showing the scene at the end of the video; upload it here Reviewers: * Watch https://www.youtube.com/watch?v=LjPNT1k9cqk * Confirm that the assignee has uploaded an image with graphs loaded and configured to the same scale as each other, as shown in the video * Confirm that the assignee has enrolled in the class. |
| Description |
Welcome to your first on-boarding task for the IGB core development team!
We are super excited you have joined us! We hope you will enjoy your time with us and will make big contributions to the code base and the IGB community. For the next steps, please do the following: # Go to https://canvas.instructure.com and make a free account. # Log in and enroll in https://canvas.instructure.com/courses/1164217 # In Module I of the course, read: *IGB Background* and *Intro to IGB Data Visualization* # Download and install the current release of IGB onto your computer. # Using IGB, copy the actions shown in this IGB video: https://www.youtube.com/watch?v=LjPNT1k9cqk # Re-create the scene shown at the very end of the video. # Use the camera button in the IGB toolbar to take a picture of IGB showing the scene at the end of the video; upload it here Reviewers: * Watch https://www.youtube.com/watch?v=LjPNT1k9cqk * Confirm that the assignee has uploaded an image with graphs loaded and configured to the same scale as each other, as shown in the video * Confirm that the assignee has enrolled in the class. |
Welcome to your first on-boarding task for the IGB core development team!
We are super excited you have joined us! We hope you will enjoy your time with us and will make big contributions to the code base and the IGB community. For the next steps, please do the following: # Go to https://canvas.instructure.com and make a free account. # Log in and enroll in https://canvas.instructure.com/courses/1164217 # In Module I of the course, read: *IGB Background* and *Intro to IGB Data Visualization* # Download and install the current release of IGB onto your computer. # Using IGB, copy the actions shown in this video: https://www.youtube.com/watch?v=LjPNT1k9cqk # Re-create the scene shown at the very end of the video. # Use the camera button in the IGB toolbar to take a picture of IGB showing the scene at the end of the video; upload it here Reviewers: * Watch https://www.youtube.com/watch?v=LjPNT1k9cqk * Confirm that the assignee has uploaded an image with graphs loaded and configured to the same scale as each other, as shown in the video * Confirm that the assignee has enrolled in the class. |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
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.
| Attachment | igb.png [ 14880 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
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.
| Attachment | igb2.png [ 14881 ] |
[~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!
| Sprint | Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep [ 100, 101, 102, 103 ] | Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct [ 100, 101, 102, 103, 104 ] |
| Rank | Ranked higher |
| Assignee | Irvin Naylor [ inaylor ] | Ann Loraine [ aloraine ] |
| Attachment | igb.png [ 14880 ] |
Moving to closed. Thank you for the feedback!
| 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 | Ann Loraine [ aloraine ] | Irvin Naylor [ inaylor ] |
| Description |
Welcome to your first on-boarding task for the IGB core development team!
We are super excited you have joined us! We hope you will enjoy your time with us and will make big contributions to the code base and the IGB community. For the next steps, please do the following: # Go to https://canvas.instructure.com and make a free account. # Log in and enroll in https://canvas.instructure.com/courses/1164217 # In Module I of the course, read: *IGB Background* and *Intro to IGB Data Visualization* # Download and install the current release of IGB onto your computer. # Using IGB, copy the actions shown in this video: https://www.youtube.com/watch?v=LjPNT1k9cqk # Re-create the scene shown at the very end of the video. # Use the camera button in the IGB toolbar to take a picture of IGB showing the scene at the end of the video; upload it here Reviewers: * Watch https://www.youtube.com/watch?v=LjPNT1k9cqk * Confirm that the assignee has uploaded an image with graphs loaded and configured to the same scale as each other, as shown in the video * Confirm that the assignee has enrolled in the class. |
Welcome to your first on-boarding task for the IGB core development team!
We are super excited you have joined us! We hope you will enjoy your time with us and will make big contributions to the code base and the IGB community. For the next steps, please do the following: # Log in and enroll in https://canvas.instructure.com/courses/1164217 # In Module I of the course, read: *IGB Background* and *Intro to IGB Data Visualization* #* Click on *Modules* on the left side and read the two introduction pages: *IGB Background* and *Intro to IGB Data Visualization*. # Download and install the current release of IGB onto your computer. #* To do this go to https://www.bioviz.org/ #* Click the “install IGB” button in the top right #* The appropriate version for your operating system should be supplied for you #* If you need a different version, click the *Click here for other ways to download IGB* hyperlink to see downloadable versions of IGB for other operating systems. #* Click the button to download IGB for your computer #* Run the downloaded file #* Follow the instructions in the setup wizard. #* Open and run the Integrated Genome Browser software. #* The IGB Quickstart webpage will open automatically in your web browser. #* IGB may take several seconds to launch. # Using IGB, follow along and copy the actions shown in this video: https://www.youtube.com/watch?v=LjPNT1k9cqk # Re-create the scene shown at the very end of the video. # Then use the camera icon button in the IGB toolbar at the top, or go to *File > Save Image* to take a picture of IGB showing the scene at the end of the video; # Upload that image here as an attachment (you can use the plus icon to the right of *Attachments*). # Move the ticket to *Needs 1st Level Review* by clicking the *Workflow* dropdown button at the top (under the ticket name), and select *Request Review*. You could also drag the ticket over to the right one space from the *Agile board > IGB > Work view*. # Since this might be the first ticket you do, and it needs to be completed before you move on to On-Boarding: Step 1 (Step 0 is a blocker for Step 1): Reach out to another developer here to review your ticket with you before you move on. Reviewers: * Watch https://www.youtube.com/watch?v=LjPNT1k9cqk * Confirm that the assignee has uploaded an image with graphs loaded and configured to the same scale as each other, as shown in the video * Confirm that the assignee has enrolled in the class. To do this select the *People* tab and look for the student’s name in the list. |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Assignee | Irvin Naylor [ inaylor ] | Omkar Marne [ omarne ] |
| Description |
Welcome to your first on-boarding task for the IGB core development team!
We are super excited you have joined us! We hope you will enjoy your time with us and will make big contributions to the code base and the IGB community. For the next steps, please do the following: # Log in and enroll in https://canvas.instructure.com/courses/1164217 # In Module I of the course, read: *IGB Background* and *Intro to IGB Data Visualization* #* Click on *Modules* on the left side and read the two introduction pages: *IGB Background* and *Intro to IGB Data Visualization*. # Download and install the current release of IGB onto your computer. #* To do this go to https://www.bioviz.org/ #* Click the “install IGB” button in the top right #* The appropriate version for your operating system should be supplied for you #* If you need a different version, click the *Click here for other ways to download IGB* hyperlink to see downloadable versions of IGB for other operating systems. #* Click the button to download IGB for your computer #* Run the downloaded file #* Follow the instructions in the setup wizard. #* Open and run the Integrated Genome Browser software. #* The IGB Quickstart webpage will open automatically in your web browser. #* IGB may take several seconds to launch. # Using IGB, follow along and copy the actions shown in this video: https://www.youtube.com/watch?v=LjPNT1k9cqk # Re-create the scene shown at the very end of the video. # Then use the camera icon button in the IGB toolbar at the top, or go to *File > Save Image* to take a picture of IGB showing the scene at the end of the video; # Upload that image here as an attachment (you can use the plus icon to the right of *Attachments*). # Move the ticket to *Needs 1st Level Review* by clicking the *Workflow* dropdown button at the top (under the ticket name), and select *Request Review*. You could also drag the ticket over to the right one space from the *Agile board > IGB > Work view*. # Since this might be the first ticket you do, and it needs to be completed before you move on to On-Boarding: Step 1 (Step 0 is a blocker for Step 1): Reach out to another developer here to review your ticket with you before you move on. Reviewers: * Watch https://www.youtube.com/watch?v=LjPNT1k9cqk * Confirm that the assignee has uploaded an image with graphs loaded and configured to the same scale as each other, as shown in the video * Confirm that the assignee has enrolled in the class. To do this select the *People* tab and look for the student’s name in the list. |
Welcome to your first on-boarding task for the IGB core development team!
We are super excited you have joined us! We hope you will enjoy your time with us and will make big contributions to the code base and the IGB community. For the next steps, please do the following tasks to get familiar with IGB and how it is used. Note that this issue has 3 story points. A "story point" is an estimate for how long a task ought to take. One day is roughly equal to one story point. This means you should expect to spend about three working days on this "on-boarding" task. Take your time on this task and explore the IGB interface to better understand how it works. Reading: IGB on-line canvas course: # Log in and enroll in https://canvas.instructure.com/courses/1164217 # In Module I of the course, read: *IGB Background* and *Intro to IGB Data Visualization* #* Click on *Modules* on the left side and read the two introduction pages: *IGB Background* and *Intro to IGB Data Visualization*. IGB documentation: # Visit the IGB user's guide and get familiar with all the contents: https://wiki.transvar.org/display/igbman/Home # Visit the IGB Release Documentation guide, which we use for testing new released. Get familiar with the contents: https://wiki.transvar.org/display/ITD/IGB+Release+Documentation # Visit the IGB Developers guide and get familiar with the contents: https://wiki.transvar.org/display/igbdevelopers/Home Get started using IGB: # Download and install the current release of IGB onto your computer from https://bioviz.org/ #* Click the “install IGB” button in the top right #* The appropriate version for your operating system should be supplied for you #* If you need a different version, click the *Click here for other ways to download IGB* hyperlink to see downloadable versions of IGB for other operating systems. #* Click the button to download IGB for your computer #* Run the downloaded file #* Follow the instructions in the setup wizard. #* Open and run the Integrated Genome Browser software. #* The IGB Quickstart webpage will open automatically in your web browser. #* IGB may take several seconds to launch. # Using IGB, follow along and copy the actions shown in this video: https://www.youtube.com/watch?v=LjPNT1k9cqk # Re-create the scene shown at the very end of the video. # Then use the camera icon button in the IGB toolbar at the top, or go to *File > Save Image* to take a picture of IGB showing the scene at the end of the video; # Upload that image here as an attachment (you can use the plus icon to the right of *Attachments*). # Move the ticket to *Needs 1st Level Review* by clicking the *Workflow* dropdown button at the top (under the ticket name), and select *Request Review*. You could also drag the ticket over to the right one space from the *Agile board > IGB > Work view*. # Since this might be the first ticket you do, and it needs to be completed before you move on to On-Boarding: Step 1 (Step 0 is a blocker for Step 1): Reach out to another developer here to review your ticket with you before you move on. Reviewers: * Watch https://www.youtube.com/watch?v=LjPNT1k9cqk * Confirm that the assignee has uploaded an image with graphs loaded and configured to the same scale as each other, as shown in the video * Confirm that the assignee has enrolled in the class. To do this select the *People* tab and look for the student’s name in the list. |
| Description |
Welcome to your first on-boarding task for the IGB core development team!
We are super excited you have joined us! We hope you will enjoy your time with us and will make big contributions to the code base and the IGB community. For the next steps, please do the following tasks to get familiar with IGB and how it is used. Note that this issue has 3 story points. A "story point" is an estimate for how long a task ought to take. One day is roughly equal to one story point. This means you should expect to spend about three working days on this "on-boarding" task. Take your time on this task and explore the IGB interface to better understand how it works. Reading: IGB on-line canvas course: # Log in and enroll in https://canvas.instructure.com/courses/1164217 # In Module I of the course, read: *IGB Background* and *Intro to IGB Data Visualization* #* Click on *Modules* on the left side and read the two introduction pages: *IGB Background* and *Intro to IGB Data Visualization*. IGB documentation: # Visit the IGB user's guide and get familiar with all the contents: https://wiki.transvar.org/display/igbman/Home # Visit the IGB Release Documentation guide, which we use for testing new released. Get familiar with the contents: https://wiki.transvar.org/display/ITD/IGB+Release+Documentation # Visit the IGB Developers guide and get familiar with the contents: https://wiki.transvar.org/display/igbdevelopers/Home Get started using IGB: # Download and install the current release of IGB onto your computer from https://bioviz.org/ #* Click the “install IGB” button in the top right #* The appropriate version for your operating system should be supplied for you #* If you need a different version, click the *Click here for other ways to download IGB* hyperlink to see downloadable versions of IGB for other operating systems. #* Click the button to download IGB for your computer #* Run the downloaded file #* Follow the instructions in the setup wizard. #* Open and run the Integrated Genome Browser software. #* The IGB Quickstart webpage will open automatically in your web browser. #* IGB may take several seconds to launch. # Using IGB, follow along and copy the actions shown in this video: https://www.youtube.com/watch?v=LjPNT1k9cqk # Re-create the scene shown at the very end of the video. # Then use the camera icon button in the IGB toolbar at the top, or go to *File > Save Image* to take a picture of IGB showing the scene at the end of the video; # Upload that image here as an attachment (you can use the plus icon to the right of *Attachments*). # Move the ticket to *Needs 1st Level Review* by clicking the *Workflow* dropdown button at the top (under the ticket name), and select *Request Review*. You could also drag the ticket over to the right one space from the *Agile board > IGB > Work view*. # Since this might be the first ticket you do, and it needs to be completed before you move on to On-Boarding: Step 1 (Step 0 is a blocker for Step 1): Reach out to another developer here to review your ticket with you before you move on. Reviewers: * Watch https://www.youtube.com/watch?v=LjPNT1k9cqk * Confirm that the assignee has uploaded an image with graphs loaded and configured to the same scale as each other, as shown in the video * Confirm that the assignee has enrolled in the class. To do this select the *People* tab and look for the student’s name in the list. |
Welcome to your first on-boarding task for the IGB core development team!
We are super excited you have joined us! We hope you will enjoy your time with us and will make big contributions to the code base and the IGB community. For the next steps, please do the following tasks to get familiar with IGB and how it is used. Note that this issue has 3 story points. A "story point" is an estimate for how long a task ought to take. One day is roughly equal to one story point. This means you should expect to spend about three working days on this "on-boarding" task. Take your time on this task and explore the IGB interface to better understand how it works. Reading: IGB on-line canvas course: * Enroll in https://canvas.instructure.com/courses/1164217 * In Module I of the course, read: *IGB Background* and *Intro to IGB Data Visualization* IGB documentation: * Visit the IGB user's guide and get familiar with all the contents: https://wiki.transvar.org/display/igbman/Home * Visit the IGB Release Documentation guide, which we use for testing new released. Get familiar with the contents: https://wiki.transvar.org/display/ITD/IGB+Release+Documentation * Visit the IGB Developers guide and get familiar with the contents: https://wiki.transvar.org/display/igbdevelopers/Home Get started using IGB: # Download and install the current release of IGB onto your computer from https://bioviz.org/ #* Click the “install IGB” button in the top right #* The appropriate version for your operating system should be supplied for you #* If you need a different version, click the *Click here for other ways to download IGB* hyperlink to see downloadable versions of IGB for other operating systems. #* Click the button to download IGB for your computer #* Run the downloaded file #* Follow the instructions in the setup wizard. #* Open and run the Integrated Genome Browser software. #* The IGB Quickstart webpage will open automatically in your web browser. #* IGB may take several seconds to launch. # Using IGB, follow along and copy the actions shown in this video: https://www.youtube.com/watch?v=LjPNT1k9cqk # Re-create the scene shown at the very end of the video. # Then use the camera icon button in the IGB toolbar at the top, or go to *File > Save Image* to take a picture of IGB showing the scene at the end of the video; # Upload that image here as an attachment (you can use the plus icon to the right of *Attachments*). # Move the ticket to *Needs 1st Level Review* by clicking the *Workflow* dropdown button at the top (under the ticket name), and select *Request Review*. You could also drag the ticket over to the right one space from the *Agile board > IGB > Work view*. # Since this might be the first ticket you do, and it needs to be completed before you move on to On-Boarding: Step 1 (Step 0 is a blocker for Step 1): Reach out to another developer here to review your ticket with you before you move on. Reviewers: * Watch https://www.youtube.com/watch?v=LjPNT1k9cqk * Confirm that the assignee has uploaded an image with graphs loaded and configured to the same scale as each other, as shown in the video * Confirm that the assignee has enrolled in the class. To do this select the *People* tab and look for the student’s name in the list. |
| Description |
Welcome to your first on-boarding task for the IGB core development team!
We are super excited you have joined us! We hope you will enjoy your time with us and will make big contributions to the code base and the IGB community. For the next steps, please do the following tasks to get familiar with IGB and how it is used. Note that this issue has 3 story points. A "story point" is an estimate for how long a task ought to take. One day is roughly equal to one story point. This means you should expect to spend about three working days on this "on-boarding" task. Take your time on this task and explore the IGB interface to better understand how it works. Reading: IGB on-line canvas course: * Enroll in https://canvas.instructure.com/courses/1164217 * In Module I of the course, read: *IGB Background* and *Intro to IGB Data Visualization* IGB documentation: * Visit the IGB user's guide and get familiar with all the contents: https://wiki.transvar.org/display/igbman/Home * Visit the IGB Release Documentation guide, which we use for testing new released. Get familiar with the contents: https://wiki.transvar.org/display/ITD/IGB+Release+Documentation * Visit the IGB Developers guide and get familiar with the contents: https://wiki.transvar.org/display/igbdevelopers/Home Get started using IGB: # Download and install the current release of IGB onto your computer from https://bioviz.org/ #* Click the “install IGB” button in the top right #* The appropriate version for your operating system should be supplied for you #* If you need a different version, click the *Click here for other ways to download IGB* hyperlink to see downloadable versions of IGB for other operating systems. #* Click the button to download IGB for your computer #* Run the downloaded file #* Follow the instructions in the setup wizard. #* Open and run the Integrated Genome Browser software. #* The IGB Quickstart webpage will open automatically in your web browser. #* IGB may take several seconds to launch. # Using IGB, follow along and copy the actions shown in this video: https://www.youtube.com/watch?v=LjPNT1k9cqk # Re-create the scene shown at the very end of the video. # Then use the camera icon button in the IGB toolbar at the top, or go to *File > Save Image* to take a picture of IGB showing the scene at the end of the video; # Upload that image here as an attachment (you can use the plus icon to the right of *Attachments*). # Move the ticket to *Needs 1st Level Review* by clicking the *Workflow* dropdown button at the top (under the ticket name), and select *Request Review*. You could also drag the ticket over to the right one space from the *Agile board > IGB > Work view*. # Since this might be the first ticket you do, and it needs to be completed before you move on to On-Boarding: Step 1 (Step 0 is a blocker for Step 1): Reach out to another developer here to review your ticket with you before you move on. Reviewers: * Watch https://www.youtube.com/watch?v=LjPNT1k9cqk * Confirm that the assignee has uploaded an image with graphs loaded and configured to the same scale as each other, as shown in the video * Confirm that the assignee has enrolled in the class. To do this select the *People* tab and look for the student’s name in the list. |
Welcome to your first on-boarding task for the IGB core development team!
We are super excited you have joined us! We hope you will enjoy your time with us and will make big contributions to the code base and the IGB community. For the next steps, please do the following tasks to get familiar with IGB and how it is used. Note that this issue has 3 story points. A "story point" is an estimate for how long a task ought to take. One day is roughly equal to one story point. This means you should expect to spend about three working days on this "on-boarding" task. Take your time on this task and explore the IGB interface to better understand how it works. Reading: IGB on-line canvas course: * Enroll in https://canvas.instructure.com/courses/1164217 * In Module I of the course, read: *IGB Background* and *Intro to IGB Data Visualization* IGB documentation: * Visit the IGB user's guide and get familiar with all the contents: https://wiki.transvar.org/display/igbman/Home * Visit the IGB Release Documentation guide, which we use for testing new released. Get familiar with the contents: https://wiki.transvar.org/display/ITD/IGB+Release+Documentation * Visit the IGB Developers guide and get familiar with the contents: https://wiki.transvar.org/display/igbdevelopers/Home Get started using IGB: # Download and install the current release of IGB onto your computer from https://bioviz.org/ # Click the “install IGB” button in the top right. (The appropriate version for your operating system should be supplied for you.) # Click the button to download IGB for your computer # Run the downloaded file # Follow the instructions in the setup wizard. # Open and run the Integrated Genome Browser software. # The IGB Quickstart webpage will open automatically in your web browser. # IGB may take several seconds to launch. # Using IGB, follow along and copy the actions shown in this video: https://www.youtube.com/watch?v=LjPNT1k9cqk # Re-create the scene shown at the very end of the video. # Then use the camera icon button in the IGB toolbar at the top, or go to *File > Save Image* to take a picture of IGB showing the scene at the end of the video; # Upload that image here as an attachment (you can use the plus icon to the right of *Attachments*). # Move the ticket to *Needs 1st Level Review* by clicking the *Workflow* dropdown button at the top (under the ticket name), and select *Request Review*. You could also drag the ticket over to the right one space from the *Agile board > IGB > Work view*. # Since this might be the first ticket you do, and it needs to be completed before you move on to On-Boarding: Step 1 (Step 0 is a blocker for Step 1): Reach out to another developer here to review your ticket with you before you move on. Reviewers: * Watch https://www.youtube.com/watch?v=LjPNT1k9cqk * Confirm that the assignee has uploaded an image with graphs loaded and configured to the same scale as each other, as shown in the video * Confirm that the assignee has enrolled in the class. To do this select the *People* tab and look for the student’s name in the list. |
| Sprint | Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct [ 100, 101, 102, 103, 104 ] | Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Winter 3 Jan 25 - Feb 5 [ 100, 101, 102, 103, 104, 113 ] |
| 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 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | IGB.PNG [ 15138 ] |
| Attachment | IGB.PNG [ 15138 ] |
| Attachment | IGB.PNG [ 15139 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Omkar Marne [ omarne ] | Ann Loraine [ aloraine ] |
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.
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] | Omkar Marne [ omarne ] |
My apologies. I went through the course without enrolling. Please check if my name in the list now.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | IGB.PNG [ 15139 ] |
IGB
| Attachment | IGB.PNG [ 15140 ] |
I have uploaded the corrected image. I was able to do 'SELECT ALL' and change the X and Y axis for the coverage graphs.
| Attachment | IGB.PNG [ 15140 ] |
| Attachment | IGB.PNG [ 15141 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Omkar Marne [ omarne ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Sai Supreeth Segu [ ssegu ] |
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.
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Sai Supreeth Segu [ ssegu ] | Omkar Marne [ omarne ] |
| Attachment | IGB.PNG [ 15141 ] |
IGB updated image
| Attachment | IGB.PNG [ 15142 ] |
Please check the corrected IGB image.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Omkar Marne [ omarne ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Sai Supreeth Segu Please check the corrected IGB image and let me know if its wrong.
| Assignee | Sai Supreeth Segu [ ssegu ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Omkar Marne Screenshot looks good to me. Moving the ticket to pull request
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Sai Supreeth Segu [ ssegu ] |
Thank you Sai Supreeth Segu
| Sprint | Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Winter 3 Jan 25 - Feb 5 [ 100, 101, 102, 103, 104, 113 ] | Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19 [ 100, 101, 102, 103, 104, 113, 114 ] |
| Rank | Ranked higher |
| Sprint | Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19 [ 100, 101, 102, 103, 104, 113, 114 ] | Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5 [ 100, 101, 102, 103, 104, 113, 114, 115 ] |
| Rank | Ranked higher |
| 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 | Jay Ostwal [ jayostwal ] |
| Sprint | Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5 [ 100, 101, 102, 103, 104, 113, 114, 115 ] | Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 3 2021 Apr 19 - Apr 30 [ 100, 101, 102, 103, 104, 113, 114, 115, 119 ] |
| Attachment | igb.png [ 15950 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Jay Ostwal [ jayostwal ] |
| Assignee | Irvin Naylor [ inaylor ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| 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 | Irvin Naylor [ inaylor ] | Jay Ostwal [ jayostwal ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Assignee | Jay Ostwal [ jayostwal ] |
| Sprint | Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 3 2021 Apr 19 - Apr 30 [ 100, 101, 102, 103, 104, 113, 114, 115, 119 ] | Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 3 2021 Apr 19 - Apr 30, Summer 1 2023 May 15 [ 100, 101, 102, 103, 104, 113, 114, 115, 119, 170 ] |
| Assignee | Kaushik Gopu [ kgopu ] |
| Description |
Welcome to your first on-boarding task for the IGB core development team!
We are super excited you have joined us! We hope you will enjoy your time with us and will make big contributions to the code base and the IGB community. For the next steps, please do the following tasks to get familiar with IGB and how it is used. Note that this issue has 3 story points. A "story point" is an estimate for how long a task ought to take. One day is roughly equal to one story point. This means you should expect to spend about three working days on this "on-boarding" task. Take your time on this task and explore the IGB interface to better understand how it works. Reading: IGB on-line canvas course: * Enroll in https://canvas.instructure.com/courses/1164217 * In Module I of the course, read: *IGB Background* and *Intro to IGB Data Visualization* IGB documentation: * Visit the IGB user's guide and get familiar with all the contents: https://wiki.transvar.org/display/igbman/Home * Visit the IGB Release Documentation guide, which we use for testing new released. Get familiar with the contents: https://wiki.transvar.org/display/ITD/IGB+Release+Documentation * Visit the IGB Developers guide and get familiar with the contents: https://wiki.transvar.org/display/igbdevelopers/Home Get started using IGB: # Download and install the current release of IGB onto your computer from https://bioviz.org/ # Click the “install IGB” button in the top right. (The appropriate version for your operating system should be supplied for you.) # Click the button to download IGB for your computer # Run the downloaded file # Follow the instructions in the setup wizard. # Open and run the Integrated Genome Browser software. # The IGB Quickstart webpage will open automatically in your web browser. # IGB may take several seconds to launch. # Using IGB, follow along and copy the actions shown in this video: https://www.youtube.com/watch?v=LjPNT1k9cqk # Re-create the scene shown at the very end of the video. # Then use the camera icon button in the IGB toolbar at the top, or go to *File > Save Image* to take a picture of IGB showing the scene at the end of the video; # Upload that image here as an attachment (you can use the plus icon to the right of *Attachments*). # Move the ticket to *Needs 1st Level Review* by clicking the *Workflow* dropdown button at the top (under the ticket name), and select *Request Review*. You could also drag the ticket over to the right one space from the *Agile board > IGB > Work view*. # Since this might be the first ticket you do, and it needs to be completed before you move on to On-Boarding: Step 1 (Step 0 is a blocker for Step 1): Reach out to another developer here to review your ticket with you before you move on. Reviewers: * Watch https://www.youtube.com/watch?v=LjPNT1k9cqk * Confirm that the assignee has uploaded an image with graphs loaded and configured to the same scale as each other, as shown in the video * Confirm that the assignee has enrolled in the class. To do this select the *People* tab and look for the student’s name in the list. |
Welcome to your first on-boarding task for the IGB core development team!
We are super excited you have joined us! We hope you will enjoy your time with us and will make big contributions to the code base and the IGB community. For the next steps, please do the following tasks to get familiar with IGB and how it is used. Note that this issue has 3 story points. A "story point" is an estimate for how long a task ought to take. One day is roughly equal to one story point. This means you should expect to spend about three working days on this "on-boarding" task. Take your time on this task and explore the IGB interface to better understand how it works. Reading: IGB on-line canvas course: * Enroll in https://canvas.instructure.com/courses/1164217 * In Module I of the course, read: *IGB Background* and *Intro to IGB Data Visualization* IGB documentation: * Visit the IGB user's guide and get familiar with all the contents: https://wiki.bioviz.org/confluence/display/igbman/Home * Visit the IGB Release Documentation guide, which we use for testing new released. Get familiar with the contents: https://wiki.bioviz.org/confluence/display/ITD/IGB+Release+Documentation * Visit the IGB Developers guide and get familiar with the contents: https://wiki.bioviz.org/confluence/display/igbdevelopers/Home Get started using IGB: # Download and install the current release of IGB onto your computer from https://bioviz.org/ # Click the “install IGB” button in the top right. (The appropriate version for your operating system should be supplied for you.) # Click the button to download IGB for your computer # Run the downloaded file # Follow the instructions in the setup wizard. # Open and run the Integrated Genome Browser software. # The IGB Quickstart webpage will open automatically in your web browser. # IGB may take several seconds to launch. # Using IGB, follow along and copy the actions shown in this video: https://www.youtube.com/watch?v=LjPNT1k9cqk # Re-create the scene shown at the very end of the video. # Then use the camera icon button in the IGB toolbar at the top, or go to *File > Save Image* to take a picture of IGB showing the scene at the end of the video; # Upload that image here as an attachment (you can use the plus icon to the right of *Attachments*). # Move the ticket to *Needs 1st Level Review* by clicking the *Workflow* dropdown button at the top (under the ticket name), and select *Request Review*. You could also drag the ticket over to the right one space from the *Agile board > IGB > Work view*. # Since this might be the first ticket you do, and it needs to be completed before you move on to On-Boarding: Step 1 (Step 0 is a blocker for Step 1): Reach out to another developer here to review your ticket with you before you move on. Reviewers: * Watch https://www.youtube.com/watch?v=LjPNT1k9cqk * Confirm that the assignee has uploaded an image with graphs loaded and configured to the same scale as each other, as shown in the video * Confirm that the assignee has enrolled in the class. To do this select the *People* tab and look for the student’s name in the list. |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | igb_1.0.png [ 17884 ] |
| 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 | Kaushik Gopu [ kgopu ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Sprint | Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 3 2021 Apr 19 - Apr 30, Summer 1 2023 May 15 [ 100, 101, 102, 103, 104, 113, 114, 115, 119, 170 ] | Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 3 2021 Apr 19 - Apr 30, Summer 1 2023 May 15, Fall 3 2023 Oct 2 [ 100, 101, 102, 103, 104, 113, 114, 115, 119, 170, 179 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | igb.png [ 18052 ] |
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
| Description |
Welcome to your first on-boarding task for the IGB core development team!
We are super excited you have joined us! We hope you will enjoy your time with us and will make big contributions to the code base and the IGB community. For the next steps, please do the following tasks to get familiar with IGB and how it is used. Note that this issue has 3 story points. A "story point" is an estimate for how long a task ought to take. One day is roughly equal to one story point. This means you should expect to spend about three working days on this "on-boarding" task. Take your time on this task and explore the IGB interface to better understand how it works. Reading: IGB on-line canvas course: * Enroll in https://canvas.instructure.com/courses/1164217 * In Module I of the course, read: *IGB Background* and *Intro to IGB Data Visualization* IGB documentation: * Visit the IGB user's guide and get familiar with all the contents: https://wiki.bioviz.org/confluence/display/igbman/Home * Visit the IGB Release Documentation guide, which we use for testing new released. Get familiar with the contents: https://wiki.bioviz.org/confluence/display/ITD/IGB+Release+Documentation * Visit the IGB Developers guide and get familiar with the contents: https://wiki.bioviz.org/confluence/display/igbdevelopers/Home Get started using IGB: # Download and install the current release of IGB onto your computer from https://bioviz.org/ # Click the “install IGB” button in the top right. (The appropriate version for your operating system should be supplied for you.) # Click the button to download IGB for your computer # Run the downloaded file # Follow the instructions in the setup wizard. # Open and run the Integrated Genome Browser software. # The IGB Quickstart webpage will open automatically in your web browser. # IGB may take several seconds to launch. # Using IGB, follow along and copy the actions shown in this video: https://www.youtube.com/watch?v=LjPNT1k9cqk # Re-create the scene shown at the very end of the video. # Then use the camera icon button in the IGB toolbar at the top, or go to *File > Save Image* to take a picture of IGB showing the scene at the end of the video; # Upload that image here as an attachment (you can use the plus icon to the right of *Attachments*). # Move the ticket to *Needs 1st Level Review* by clicking the *Workflow* dropdown button at the top (under the ticket name), and select *Request Review*. You could also drag the ticket over to the right one space from the *Agile board > IGB > Work view*. # Since this might be the first ticket you do, and it needs to be completed before you move on to On-Boarding: Step 1 (Step 0 is a blocker for Step 1): Reach out to another developer here to review your ticket with you before you move on. Reviewers: * Watch https://www.youtube.com/watch?v=LjPNT1k9cqk * Confirm that the assignee has uploaded an image with graphs loaded and configured to the same scale as each other, as shown in the video * Confirm that the assignee has enrolled in the class. To do this select the *People* tab and look for the student’s name in the list. |
Welcome to your first on-boarding task for the IGB core development team!
We are super excited you have joined us! We hope you will enjoy your time with us and will make big contributions to the code base and the IGB community. For the next steps, please do the following tasks to get familiar with IGB and how it is used. Note that this issue has 3 story points. A "story point" is an estimate for how long a task ought to take. One day is roughly equal to one story point. This means you should expect to spend about three working days on this "on-boarding" task. Take your time on this task and explore the IGB interface to better understand how it works. Reading: IGB on-line canvas course: * Enroll in https://canvas.instructure.com/courses/1164217 * In Module I of the course, read: *IGB Background* and *Intro to IGB Data Visualization* IGB documentation: * Visit the IGB user's guide and get familiar with all the contents: https://wiki.bioviz.org/confluence/display/igbman/Home * Visit the IGB Release Documentation guide, which we use for testing new released. Get familiar with the contents: https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first * Visit the IGB Developers guide and get familiar with the contents: https://wiki.bioviz.org/confluence/display/igbdevelopers/Developing+Integrated+Genome+Browser Get started using IGB: # Download and install the current release of IGB onto your computer from https://bioviz.org/ # Click the “install IGB” button in the top right. (The appropriate version for your operating system should be supplied for you.) # Click the button to download IGB for your computer # Run the downloaded file # Follow the instructions in the setup wizard. # Open and run the Integrated Genome Browser software. # The IGB Quickstart webpage will open automatically in your web browser. # IGB may take several seconds to launch. # Using IGB, follow along and copy the actions shown in this video: https://www.youtube.com/watch?v=LjPNT1k9cqk # Re-create the scene shown at the very end of the video. # Then use the camera icon button in the IGB toolbar at the top, or go to *File > Save Image* to take a picture of IGB showing the scene at the end of the video; # Upload that image here as an attachment (you can use the plus icon to the right of *Attachments*). # Move the ticket to *Needs 1st Level Review* by clicking the *Workflow* dropdown button at the top (under the ticket name), and select *Request Review*. You could also drag the ticket over to the right one space from the *Agile board > IGB > Work view*. # Since this might be the first ticket you do, and it needs to be completed before you move on to On-Boarding: Step 1 (Step 0 is a blocker for Step 1): Reach out to another developer here to review your ticket with you before you move on. Reviewers: * Watch https://www.youtube.com/watch?v=LjPNT1k9cqk * Confirm that the assignee has uploaded an image with graphs loaded and configured to the same scale as each other, as shown in the video * Confirm that the assignee has enrolled in the class. To do this select the *People* tab and look for the student’s name in the list. |
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.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] | Ann Loraine [ aloraine ] |
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 
| Assignee | Ann Loraine [ aloraine ] |
| Attachment | igb.png [ 18052 ] |
| Attachment | igb.png [ 18053 ] |
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
.
| Assignee | Molly Davis [ molly ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
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!
| 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 | Molly Davis [ molly ] | Jaya Sravani Sirigineedi [ jsirigin ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Sprint | Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 3 2021 Apr 19 - Apr 30, Summer 1 2023 May 15, Fall 3 2023 Oct 2 [ 100, 101, 102, 103, 104, 113, 114, 115, 119, 170, 179 ] | Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 3 2021 Apr 19 - Apr 30, Summer 1 2023 May 15, Fall 3 2023 Oct 2, Fall 4 [ 100, 101, 102, 103, 104, 113, 114, 115, 119, 170, 179, 205 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] | Udaya Chinta [ uchinta ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | screenshot-1.png [ 18536 ] |
| Attachment | screenshot-2.png [ 18537 ] |
*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?
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Udaya Chinta [ uchinta ] | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] |
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.
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Udaya Chinta [ uchinta ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | screenshot-3.png [ 18545 ] |
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
| Assignee | Udaya Chinta [ uchinta ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Sprint | Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 3 2021 Apr 19 - Apr 30, Summer 1 2023 May 15, Fall 3 2023 Oct 2, Fall 4 [ 100, 101, 102, 103, 104, 113, 114, 115, 119, 170, 179, 205 ] | Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 3 2021 Apr 19 - Apr 30, Summer 1 2023 May 15, Fall 3 2023 Oct 2, Fall 4, Fall 5 [ 100, 101, 102, 103, 104, 113, 114, 115, 119, 170, 179, 205, 206 ] |
| Rank | Ranked higher |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
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.
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] | Udaya Chinta [ uchinta ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Udaya Chinta [ uchinta ] | Jaya Sravani Sirigineedi [ jsirigin ] |
| 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 | Jaya Sravani Sirigineedi [ jsirigin ] | Udaya Chinta [ uchinta ] |
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.