1. Discovery Environment Tool Integration High Level Overview

2. Definitions to keep in mind….. Tool-installed on condor cluster or via Foundational API. Binary or script. Application- GUI representation created in DE for an installed tool Analysis-act of using the application with data

3. Ways to customize applications Copy and edit app currently in DE Integrate new interface for existing binary or executable (not your own) Integrate your own command line program

4. Copy/Edit existing interface Use case: An application exists in the DE that I’d like to use, but I use different values or additional parameters for my research

5. How to do this Highlight desired application and select copy

6. How to do this Copy will open tool integration interface with copy of app

7. How to do this Selection of edit will open up interface description form

8. How to do this Selection of edit will open up interface description form

9. Hands on Goals: Copy app Modify name of app and default values Save and publish to workspace

10. Integrate a new existing application Use case: There is a tool that I use frequently in my research, and I don’t see an interface for it in the iPlant Discovery Environment – CAVEATS: must be command line tool or script that can be called via command line – Integration of a tool that is deployed via Foundation API is separate use case, and separate presentation.

11. How to do this In App Catalog, select Create New App

12. How to do this Opens Tool Integration Interface. Browse available deployed binaries/tools

13. How to do this Filter for tool of interest

14. How to do this Select tool, name it, add description and appropriate attribution

15. How to do this If tool is not yet deployed, request new installation using form

16. How to do this You can continue to create an interface for your tool, while awaiting deployment.

17. How to do this Create interface on “arguments” panel

18. How to do this When complete, publish to workspace.

19. How to do this Published application available for use

20. Hands on Goals: Successfully select tool for creating interface (use FASTX Trimmer as example) Add name and description Describe all arguments (inputs, parameters,outputs) and validations Publish to workspace and test in DE

21. Integrate MY OWN tool Use case: Research group is working on developing an application that they find useful and are about to publish. Once published, they would like to make an interface available for wider adoption.

22. How to do this Suggestions: – Install and test in Atmosphere prior to asking for deployment. Ensures will work in our condor environment and help determine additional dependencies needed. Procedure: – Request Atmosphere account (go to http://user.iplantcollaborative.org/)http://user.iplantcollaborative.org/ – Request deployment once validated and continue as per “Integrating a new existing application”.

23. Submitting for Public Use

24. Test in private workspace first Provide link to documentation Submit test datasets to support@iplantcollaborative.org support@iplantcollaborative.org App will display in Beta Category

25. For advanced use cases or tools needing HPC resources Contact support@iplantcollaborative.org