1. Extending the Discovery Environment: Tool Integration and Customization

2. Extending the Discovery Environment DE can be extended by users who wish to: Integrate a tool not already in the DE. Customize an application already in the DE. Understanding of command line applications and arguments is helpful, but no programming is required.

3. Why Extend the DE? 1.There’s a tool I use frequently in my research, but it’s not in the DE. 2.An application exists in the DE that I’d like to use, but I use different default values or additional parameters in my analyses. 3.Our group is publishing a useful command line tool. We’d like to make an interface for it and have it widely adopted.

4. Integrate an Application 1.There’s a tool I use frequently in my research, but it’s not in the DE. CAVEATS: – Must be a command line tool or script that can be called via command line. – Integration of a tool intended to execute on HPC resources is done via the Foundation API and is covered in a separate tutorial.

5. Tool Integration Process Have the tool installed in iPlant’s infrastructure. Decide which command line arguments to expose to users. Think about how to organize the parameters into logical groupings.

6. Tool Integration Process (cont.) Create a brief tool description. Specify the argument groups and the arguments within those groups (creates the tool interface). Preview the interface. Publish to your workspace. Test the application to ensure it runs correctly.

7. Request Tool Installation Apps -> Create -> New App Create New -> Request Tool Installation Fill out forms and submit. Receive response in 2-5 days.

8. Organization of Application Interfaces in DE The FASTX Trimmer interface is organized into two “argument groups,” each in its own panel: 1. input data, which has one argument. 2. options, which has three arguments. Arguments is another term for parameters.

9. Compare Command Line to Interface fastx_trimmer -f 1 -l 36 -i INFILE -o OUTFILE Outfile name is defined, but hidden from users so automated workflows can be created. Ignore this. It’s an undocumented feature of FASTX Trimmer.

10. Tool Integration: Hands-On Example: FASTX Trimmer (already installed). Warning: Save before leaving the tool integration interface or you’ll lose your work!

11. Go to Hands-On http://www.iplantcollaborative.org/umwiki

12. Tool Integration: Tips You can create the interface while waiting for the tool to be installed. You can include parameter validation, tool tips.

13. Tool Integration: Tips If you save your work part way through and close the Tool Integration interface, you may resume work: Apps > Create > New App > Back > Highlight your tool in the list > Edit Continue editing

14. Tool Integration: Tips All applications published to your workspace appear under Applications Under Development and can be edited without having to create a copy. Apps > Workspace > Applications under development > [highlight an app] > More Actions > Edit

15. Edit an Existing Application Interface 1.There’s a tool I use frequently in my research, but it’s not in the DE. 2.An application exists in the DE that I’d like to use, but I use different default values or additional parameters in my analyses. 3.Our group is publishing a useful command line tool. We’d like to make an interface for it and have it widely adopted.

16. Editing an Application In Apps catalog, highlight tool to edit. Select Copy. Opens Tool Integration interface. Highlight the application to edit. Select Edit. Make desired changes. Save, publish and test.

17. Integrating Your Own Application 1.There’s a tool I use frequently in my research, but it’s not in the DE. 2.An application exists in the DE that I’d like to use, but I use different default values or additional parameters in my analyses. 3.Our group is publishing a useful command line tool. We’d like to make an interface for it and have it widely adopted.

18. Integrating Your Own Tool Suggestions: – Install and test in Atmosphere prior to asking for deployment. – Ensures tool will work in iPlant’s environment and identify software dependencies. Procedure: – Request Atmosphere account at http://user.iplantcollaborative.org/ http://user.iplantcollaborative.org/ – After tool is working in Atmosphere, integrate it into the DE as usual (request installation, define interface, publish, test).

19. Submitting for Public Use Test in your DE workspace first. Provide link to documentation. (http://bit.ly/NXhlVD) Submit test dataset to support@iplantcollaborative.org support@iplantcollaborative.org App will appear in the Beta category of the catalog.

20. Submitting for Public Use Apps > Workspace > Applications under development > [highlight tool] > More Actions > Submit for public use Fill out and submit form.

21. Other Scenarios or Tools needing High Performance Computing Resources Contact support@iplantcollaborative.org

22. Question, Comments, Suggestions?