1. Yating Liu July 2018 G-OnRamp workshop
Use G-OnRamp to set up a collaborative annotation environment on Apollo
Yating Liu
July 2018 G-OnRamp workshop

2. Three types of user accounts on Apollo
Has system-wide administrative privileges
Create instructor accounts on Apollo for lab PIs / Faculty
Example: faculty who setup G-OnRamp and Apollo
Admin
Can create organisms (Apollo instances), user groups and user accounts on Apollo
Administrative privilege on organisms, users and user groups that you have created
Example: faculty who manage a collaborative annotation project
Instructor
Can be granted administrative / write / read / export privileges on an organism by an instructor or an admin
Example: students involved in the collaborative annotation project
User
Three types of user accounts on Apollo

3. General process of configuring the Apollo environment
Get an Apollo instructor account which uses the same address as your Galaxy account
(created by administrator)
Log into Galaxy
Create a user group
Apollo User Manager tool
Run the G-OnRamp workflow for JBrowse to create a JBrowse instance for your interested genome
Create an organism on Apollo with the JBrowse instance and grant permissions to the user group to access the organism on Apollo
Create or Update Organism tool
Create accounts for collaborative annotators
Add the annotators to the user group
Log into Apollo
Start genome annotation together

4. Galaxy tools to interface with Apollo
Requirements
Have an instructor or admin account on Apollo
Your Apollo account should use the same address as your Galaxy account
Create or Update Organism tool
Add an organism to the Apollo database
Grant administrative/write/read/export permissions to a selected user group
Apollo User Manager tool
Create Apollo users
Delete Apollo users
Create user groups
Delete user groups
Add Apollo users to a user group
Remove Apollo users from a user group
Delete an Apollo record tool
Delete an organism from Apollo
Export all annotations on the organism
Apollo uses the term “Organism” to refer to the workspace associated with the organism

5. Get an Apollo instructor account
If you are the administrator of the G-OnRamp instance
Should have an initial Apollo admin account
Log into Apollo and change the password
Update the password on supervisor configuration file at /etc/supervisor/conf.d/galaxy.conf, and restart the server
If you are not the administrator of the G-OnRamp instance
Ask the administrator to create an Apollo instructor account for you with the same address you used for your Galaxy account
The passwords for the Galaxy account and Apollo account can be different. we recommend using the same password to avoid potential confusion.

6. Apollo User Manager tool
Click on “Insert New operation”. You can choose an operation from the dropdown menu:
Create a user
Delete a user
Create a user group
Delete a user group
Add a user to a group
Remove a user from a group
Choose ”Create a user” from the drop-down menu

7. Create an instructor account with the Apollo User Manager Tool (by system administrator)
Create one account at a time
Specify user
Specify user first name
Specify user last name
To create an instructor account, select the “instructor” option from drop-down menu

8. Create an instructor account with the Apollo User Manager Tool: output (by system administrator)
Operation
First Name
Last Name
New Password
Role
Group
Add to Group
Remove from Group
Create User
galaxy_instructor
demo
mzgbkkgwrqxx
instructor

9. Create a user group Select “Create a user group”
Create a user group at a time
Specify the group name

10. Run the “G-OnRamp workflow for JBrowse” to create a JBrowse instance
RNA-Seq
reads
Sequence similarity
RNA-Seq analysis
Gene predictions
Repeats
JBrowse
Archive Creator
Transcripts / proteins from informant genome
Reference genome
assembly

11. Create an organism and grant permissions to the user group with the Create or Update Organism Tool
Specify JBrowse Output from JBrowse Archive Creator
If you want to create a new organism, select “Direct Entry” in the drop-down menu under the “Organism Common Name Source” field
Optional: specify Genus and Species
If set to public, this JBrowse instance is visible to all users on Apollo. Default is “No”
Specify the organism name that you would like to see on Apollo
Adds an organism to the Apollo database.
Give a user group read + write + export permissions to the organism

12. Update an existing organism with the Create or Update Organism Tool
Specify JBrowse Output from JBrowse Archive Creator
Choose the “Select” option in the drop-down menu for the “Organism Common Name Source” field, and then select the organism you want to update from the list
Optional: specify Genus and Species
If set public, this JBrowse is visible to all users on Apollo
Give a user group read + write + export permission to the organism

13. Create accounts for collaborative annotators (create multiple user accounts at a time)
Create a text file which include user information to create account. Then upload the text file to Galaxy
Open the Apollo User Manager tool and choose “Multiple users” under the “Manipulate a single user or multiple users” field
Specify the text file format (support CSV and Tabular)
Specify the text file

14. Create a text file to manage multiple users or user groups (examples)
Note: you have to use the exact same headers (case sensitive) in the examples
Text file for creating multiple users
Text file for creating or deleting multiple user groups
Text file for deleting multiple users
Text file for
adding to multiple users to a user group
removing multiple users from a user group

15. Output of Apollo User Manager
Operation
First Name
Last Name
New Password
Create User
Annotator1
gonramp
xgckxbdnqhnk
Annotator2
jjmvmchhjvtw
Annotator3
qbdtqfjqglsx
Annotator4
dvmcrjxdnvxw
Annotator5
fqtqdmcgwmqh

16. Add a user to the user group
Specify user
Select the group from the drop-down menu
Note: if the group doesn’t show up in the list, refresh the browser

17. Add the annotators to the user group (add multiple users to the user group at the same time)
Create a text file which include user information to create the accounts. Then upload the text file to Galaxy
Open the Apollo User Manager tool and choose “Multiple users” under the “Manipulate a single user or multiple users” field
Specify the text file format
Specify the text file

18. Genome annotation on Apollo
A) The ‘Navigation Panel’ runs along the top of the main panel
B) The ‘User-created Annotations’ panel contains the manual annotations
C) The ‘Evidence’ panel includes all evidence tracks aligned to the reference genome assembly
D) The ‘Annotator Panel’ allows curators to easily navigate the genome, and to display and export annotations
See the “Use Apollo to do collaborative genome annotation” walkthrough for details

19. View annotation report
Admin Tab:
Click on “Report::Instructor” to view the annotation report grouped by user groups. It includes:
Annotation record for each annotator within a user group
Detailed breakdown report for each annotator if you click on the username

20. View annotation report of the “D.miranda annotation” user group
Select report for user group “D.miranda annotation”
Export the report to a file in CSV / EXCEL / XML formats

21. Export the report to an Excel worksheet
Username
First Name
Last Name
User Group
Organism
Top Level Features
Genes
Transcripts
Exons
Transposable Elements
Repeat Regions
Last Updated
Annotator5
gonramp
D.miranda annotation
Drosophila miranda 6 32
5/21/18
Annotator2 3 15
Annotator3 1 5
Annotator1
Annotator4 2 12

22. Annotation details and organism breakdown for an individual annotator

23. Delete an Apollo organism
Only if you have administrative privilege to the organism
Delete an organism from Apollo
Export all the annotations for the organism
Export genome sequences
Export organism metadata
Remove the data directory (delete all data of the organism on the server)

24. Summary Three types of Apollo accounts
user, instructor, admin
General process of configuring an collaborative annotation environment on Apollo
Galaxy Apollo interaction tools
Create or Update Organism
Apollo User Manager
Delete an Apollo record

25. Walkthrough: set up a collaborative annotation environment on Apollo for Drosophila biarmipes
Get an instructor account (created by administrator) and log into Apollo
Use the Apollo User Manager to create an annotation user group
Run the G-OnRamp workflow for JBrowse to create a D. biarmipes JBrowse Archive
Use the “Create or Update Organism” tool to create a D. biarmipes Apollo workspace
Create user accounts for the collaborative annotators
Add the annotators to the user group

26. Additional slides

27. General process of configuring the Apollo environment (Add “Create or Update Organism” tool to the JBrowse workflow)
Get an Apollo instructor account which uses the same address as your Galaxy account
(created by administrator)
Log into Galaxy
Create a user group
Apollo User Manager tool
Run the G-OnRamp workflow for JBrowse/Apollo to
- Create a JBrowse instance for the genome of interests (JBrowse Archive Creator)
- Create an organism on Apollo with the JBrowse instance and grant permissions to the user group to access the organism on Apollo (Create or Update Organism tool)
Create accounts for collaborative annotators
Add the annotators to the user group
Log into Apollo
Start genome annotation together

28. G-OnRamp workflow for JBrowse/ Apollo
RNA-Seq
reads
Sequence similarity
RNA-Seq analysis
Gene predictions
Repeats
JBrowse
Archive Creator
Transcripts / proteins from informant genome
Reference genome
assembly
Create or Update Organism