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. Quality scale

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