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

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

General process of configuring the Apollo environment Get an Apollo instructor account which uses the same email 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

Galaxy tools to interface with Apollo Requirements Have an instructor or admin account on Apollo Your Apollo account should use the same email 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

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 email 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.

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

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

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

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

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

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

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

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

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

Output of Apollo User Manager Operation First Name Last Name Email New Password Create User Annotator1 gonramp annotator1@gonramp.com xgckxbdnqhnk Annotator2 annotator2@gonramp.com jjmvmchhjvtw Annotator3 annotator3@gonramp.com qbdtqfjqglsx Annotator4 annotator4@gonramp.com dvmcrjxdnvxw Annotator5 annotator5@gonramp.com fqtqdmcgwmqh

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

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

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

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

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

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.com Annotator5 gonramp D.miranda annotation Drosophila miranda 6 32 5/21/18 annotator2@gonramp.com Annotator2 3 15 annotator3@gonramp.com Annotator3 1 5 annotator1@gonramp.com Annotator1 annotator4@gonramp.com Annotator4 2 12

Annotation details and organism breakdown for an individual annotator

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)

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

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

Additional slides

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 email 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

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