Use G-OnRamp to set up a collaborative annotation environment on Apollo - PowerPoint Presentation

1. Use G-OnRamp to set up a collaborative annotation environment on ApolloYating LiuJuly 2018 G-OnRamp workshop

2. Three types of user accounts on Apollo

3. General process of configuring the Apollo environment

4. Galaxy tools to interface with ApolloRequirementsHave an instructor or admin account on ApolloYour 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 groupApollo User Manager toolCreate Apollo usersDelete Apollo usersCreate user groupsDelete user groupsAdd Apollo users to a user groupRemove Apollo users from a user groupDelete an Apollo record toolDelete an organism from ApolloExport all annotations on the organism

5. Get an Apollo instructor accountIf you are the administrator of the G-OnRamp instanceShould have an initial Apollo admin account Log into Apollo and change the passwordUpdate the password on supervisor configuration file at /etc/supervisor/conf.d/galaxy.conf, and restart the serverIf 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

6. Apollo User Manager toolChoose ”Create a user” from the drop-down menuClick on “Insert New operation”. You can choose an operation from the dropdown menu:Create a userDelete a userCreate a user groupDelete a user groupAdd a user to a groupRemove a user from a group

7. Create an instructor account with the Apollo User Manager Tool (by system administrator)Create one account at a timeSpecify user emailSpecify user first nameSpecify user last nameTo 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)OperationFirst NameLast NameEmailNew PasswordRoleGroupAdd to GroupRemove from GroupCreate Usergalaxy_instructordemogalaxy_instructor@apollo.commzgbkkgwrqxxinstructor

9. Create a user groupSelect “Create a user group”Create a user group at a timeSpecify the group name

10. Run the “G-OnRamp workflow for JBrowse” to create a JBrowse instance RNA-SeqreadsSequence similarityRNA-Seq analysisGene predictionsRepeatsJBrowseArchive CreatorTranscripts / proteins from informant genomeReference genomeassembly

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

12. Update an existing organism with the Create or Update Organism ToolSpecify JBrowse Output from JBrowse Archive CreatorIf set public, this JBrowse is visible to all users on ApolloGive a user group read + write + export permission to the organismChoose 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 listOptional: specify Genus and Species

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

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

15. Output of Apollo User ManagerOperationFirst NameLast NameEmailNew PasswordCreate UserAnnotator1gonrampannotator1@gonramp.comxgckxbdnqhnkCreate UserAnnotator2gonrampannotator2@gonramp.comjjmvmchhjvtwCreate UserAnnotator3gonrampannotator3@gonramp.comqbdtqfjqglsxCreate UserAnnotator4gonrampannotator4@gonramp.comdvmcrjxdnvxwCreate UserAnnotator5gonrampannotator5@gonramp.comfqtqdmcgwmqh

16. Add a user to the user groupSpecify user emailSelect the group from the drop-down menuNote: 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)Open the Apollo User Manager tool and choose “Multiple users” under the “Manipulate a single user or multiple users” fieldSpecify the text fileSpecify the text file formatCreate a text file which include user information to create the accounts. Then upload the text file to Galaxy

18. Genome annotation on ApolloA) The ‘Navigation Panel’ runs along the top of the main panelB) The ‘User-created Annotations’ panel contains the manual annotationsC) The ‘Evidence’ panel includes all evidence tracks aligned to the reference genome assemblyD) The ‘Annotator Panel’ allows curators to easily navigate the genome, and to display and export annotationsSee 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 groupDetailed breakdown report for each annotator if you click on the username

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

21. UsernameFirst NameLast NameUser GroupOrganismTop Level FeaturesGenesTranscriptsExonsTransposable ElementsRepeat RegionsLast Updatedannotator5@gonramp.comAnnotator5gonrampD.miranda annotationDrosophila miranda66632005/21/18annotator2@gonramp.comAnnotator2gonrampD.miranda annotationDrosophila miranda33315005/21/18annotator3@gonramp.comAnnotator3gonrampD.miranda annotationDrosophila miranda1015005/21/18annotator1@gonramp.comAnnotator1gonrampD.miranda annotationDrosophila miranda1116005/21/18annotator4@gonramp.comAnnotator4gonrampD.miranda annotationDrosophila miranda22212005/21/18Export the report to an Excel worksheet

22. Annotation details and organism breakdown for an individual annotator

23. Delete an Apollo organismDelete an organism from ApolloExport all the annotations for the organismExport genome sequencesExport organism metadataRemove the data directory (delete all data of the organism on the server)Only if you have administrative privilege to the organism

24. SummaryThree types of Apollo accountsuser, instructor, adminGeneral process of configuring an collaborative annotation environment on ApolloGalaxy Apollo interaction toolsCreate or Update OrganismApollo User ManagerDelete 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 ApolloUse the Apollo User Manager to create an annotation user group Run the G-OnRamp workflow for JBrowse to create a D. biarmipes JBrowse ArchiveUse the “Create or Update Organism” tool to create a D. biarmipes Apollo workspaceCreate 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)

28. G-OnRamp workflow for JBrowse/ ApolloRNA-SeqreadsSequence similarityRNA-Seq analysisGene predictionsRepeatsJBrowseArchive CreatorTranscripts / proteins from informant genomeReference genomeassemblyCreate or Update Organism