Discovery Environment Tool Integration

High Level Overview

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

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

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

How to do thisHighlight desired application and select copy

How to do thisCopy will open tool integration interface with copy of app

How to do thisSelection of edit will open up interface description form

How to do thisSelection of edit will open up interface description form

Hands on

Goals:• Copy app • Modify name of app and default values• Save and publish to workspace

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.

How to do thisIn App Catalog, select Create New App

How to do thisOpens Tool Integration Interface. Browse available deployed

binaries/tools

How to do thisFilter for tool of interest

How to do thisSelect tool, name it, add description and appropriate attribution

How to do thisIf tool is not yet deployed, request new installation using form

How to do thisYou can continue to create an interface for your tool, while

awaiting deployment.

How to do thisCreate interface on “arguments” panel

How to do thisWhen complete, publish to workspace.

How to do thisPublished application available for use

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

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.

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/)– Request deployment once validated and continue as per “Integrating a new

existing application”.

Submitting for Public Use

Submitting for Public Use

• Test in private workspace first• Provide link to documentation • Submit test datasets to

support@iplantcollaborative.org• App will display in Beta Category

For advanced use cases or tools needing HPC resources

Contactsupport@iplantcollaborative.org