Post on 17-Jan-2018
description
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