extending the discovery environment: tool integration and customization
TRANSCRIPT
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.
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.
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.
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.
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.
Request Tool InstallationApps -> Create -> New App
Create New -> Request Tool Installation
Fill out forms and submit.Receive response in 2-5 days.
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.
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.
Tool Integration: Hands-On
• Example: FASTX Trimmer (already installed).
• Warning: Save before leaving the tool integration interface or you’ll lose your work!
Tool Integration: Tips
• You can create the interface while waiting for the tool to be installed.
• You can include parameter validation, tool tips.
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
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
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.
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.
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.
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/– After tool is working in Atmosphere, integrate it into the
DE as usual (request installation, define interface, publish, test).
Submitting for Public Use
• Test in your DE workspace first.• Provide link to documentation.
(http://bit.ly/NXhlVD)
• Submit test dataset to [email protected]
• App will appear in the Beta category of the catalog.
Submitting for Public UseApps > Workspace > Applications under development > [highlight tool] > More Actions > Submit for public use
Fill out and submit form.
Other Scenarios or Tools needing High Performance Computing Resources