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For overview information, see Discovery Environment on the CyVerse website.


Maintenance: Tues, 28 Jan 2020


Discovery Environment         8:00am to 5:00pm MST
The Discovery Environment will be unavailable while patches and updates are applied.
        ** Currently running analyses will be terminated. Please plan accordingly.

Data Store                    8:00am to 5:00pm MST
The Data Store will be unavailable during the maintenance period.
Data Commons                  8:00am to 5:00pm MST
The Data Commons will be unavailable during the maintenance period.
Atmosphere and Cloud Services 8:00am to 5:00pm MST
Marana Cloud: Atmosphere instances in the Marana Cloud will be operational; however, you will not be able to use the Data Store within your instance, and you may not be able to access the Atmosphere web interface.
User Portal                   8:00am to 5:00pm MST
The User Portal,, will be unavailable while we perform maintenance and updates.
Agave/Science API             8:00am to 5:00pm MST
The Agave/Science API will be unavailable during this maintenance period.
DNA Subway                    8:00am to 5:00pm MST
DNA Subway will be unavailable during this maintenance period.
The following services will NOT be affected by the maintenance: CyVerse Wiki and JIRA

Keep up to date with our maintenance schedules on the CyVerse public calendar
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Using the Apps window and submitting an analysis

An app is the mechanism you use to submit an analysis.

 What's an app? tool? analysis?
  • App: Interface of a tool that has been configured and made available for use in the DE. The same tool can be used in more than one app, and may also be created by different integrators with different intents and interfaces.
  • Tool: Software program (executable binary or executable) that is installed on a server and integrated into the back end of the DE for use in DE apps.
  • Analysis: Detailed examination of data performed in the DE by selecting one or more apps to perform a desired task for the purpose of discussion or interpretation.

Within the Apps window, you open the app to use for your analysis, and then select the file or files to use, define the settings as needed, and launch the analysis. As the analysis proceeds through the job, you receive updates about its progress. Once the analysis is completed, you retrieve and analysis the results.

This page includes:

This section includes:

The root page DEmanual:@self could not be found in space Discovery Environment Manual.

Opening the Apps window

Click Apps to open the Apps window.

Category section

The Category section on the left shows the app categories, divided into three major sections:

  • Workspace apps: These apps are available only to you. The list includes the apps you are currently working on (Apps under development), your list of favorite apps, and the list of apps you have shared with other iPlant users. Select a category in this panel to display its contents in the right pane.
    • Apps under development are the apps and workflows you are in the process of creating and editing and which you yet shared.
    • Favorite Apps are the apps you frequently use.
    • My public apps are the apps and workflows you have shared with the public.
  • Public Apps: Apps that have been shared with other iPlant users as well as the apps you created and shared.
  • High-Performance Computing: The list of high-performance computing (HPC) apps that may be submitted directly to the Agave API. For more information on the Agave API, see The Agave API.
     Wondering why an app has a funny symbol or is no longer in the list?

    Apps with are disabled and currently not available for use.
    Apps with are public apps that have not yet been vetted by the CyVerse team.

    Apps with are private apps that you either you created or that have been shared with you by another user.

    If an app is no longer returned in a search query, it may have been deprecated as part of the app recategorization efforts. You can use a similar app by searching for an app with a similar name or that uses the same tool. If you are the app integrator or need access to the app from a link in a publication, contact CyVerse Support at for assistance.

    It's also possible you haven't authenticated to the HPC server. You are prompted to log in to the server when you log in to the DE, open the Apps window, or click the HPC tab. Once you have authenticated, you won't see the prompt again unless major changes to the HPC server require re-authentication, which should happen rarely. So if the app you are searching for is in the HPC list, logging in will return the app to you in search results.

App selection and information

The right section shows the path for the selected data item. as well as the list of apps within the selected folder and integrator's name. You also can view any ratings entered by other users and enter comments about the app. Select the app to use for your analysis from this section.

The selected folder is displayed above the right panel.

Apps and Workflows

At the top of the Apps window are the menus for managing apps and workflows:

Apps menu

Workflow menu

Apps search

Enter part of an app name to find the app to use.

Window icons

At the top right of each window are the window icons.

Customizing the Apps window

You can sort on any column in the Apps list, and hide or show columns to customize the look of your list.

  1. Hover over any column header in the list until a down arrow appears on the right side of the column:
  2. Click the down arrow:
    • To sort on the column, click either Sort Ascending or Sort Descending.
    • To hide or show a column, point to Columns, and then select or clear the checkbox for the column.
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