An app is the mechanism you use to submit an analysis. 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 analyze the results. You can view the Apps list by either tiles (the new default) or by list (the previous view).

Opening the Apps window

Apps menus

Apps menu

Workflow menu

Share menu

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Questions about apps?

Click (Help) at the top right of the Apps window in either view.

Refreshing the Apps window

Click    to update the Apps window.

Searching for an app or workflow

At the top of the window, you can search on part of an app or workflow name to find the app or workflow, topic, operation, HPC app, or tool to use. To learn more, see Searching for an App, Workflow, or Tool.

If you are looking for an app that is no longer available that you need to use, first search for a similar app (either by name or by tool). If you cannot find a suitable replacement, contact CyVerse Support at support@cyverse.org.

Also be aware that you must log in to the Agave server in order to view and use the list of HPC apps. If you have not yet authenticated (you'll only have to do it once or after a major upgrade but you'll be notified), click the HPC tab in the Apps list, or log out of the DE and back in, then log in when prompted to authenticate to the HPC server. For more information, see Using HPC Apps in the DE.

You also can click to read FAQs, ask and view questions in Ask CyVerse, and contact Support or submit feedback.

Managing tools

The Manage Tools menu is the hub for managing the Discovery Environment tools Docker images from which apps are created. Within this menu, you can manage (add, request installation, edit, delete, and use the tool in an app) and share the tool with specific collaborators, with the public, or keep it personal for just your use. For information on the Manage Tools menu, see Managing Tools in the DE.

Customizing the Apps window view

Switching the Apps list display

The apps that are displayed in the right panel can be viewed either in tiles view (the default) or list view (the previous display). Both views give you immediate access to the app and tool information used for the app, as well as the ability to quickly enter comments and rate the app. To switch to the other view, click Switch View at the top.

 

 

Changing the columns that are displayed

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:

About categories

In the left panel, the Categories are displayed.

Based on the EDAM ontology, categories under Topic and Operation help you more quickly find an app or workflow for the type of analysis you need to do. An app can be tagged with more than one category and can appear in more than one tab. Apps that have not yet been categorized are located in the Unclassified categories of the Topic and Operation tabs. All apps are available in search by name, integrator, and tool used for the app.

You can search for an app by name, integrator, tool used for the app, topic, or operation. Once you have authenticated to the Agave apps using your CyVerse username and password (usually required only the first time you log in to the DE and rarely thereafter), the list of HPC apps will also be displayed in search results and within the HPC tab. If the HPC app has been tagged with Topic and Operation terms, it will also show up under those tabs. 

In the right panel, you can view details about the app, such as the integrator's name, and any ratings and comments entered by other users. Click the name of the app to use for your analysis from this section.

Anchor = AppStatus (visible to staff only)

About app status

Depending on the status of the app, it may display an icon to denote its status (if no icon is displayed, the app is a public app). In the tiles view, the icon is displayed at the bottom right of the tile, while in the list view, the icon is displayed to the left of the app name.

Requesting a new or different category

You can request that a public app be added to a different or additional category, or suggest addition of a new category. If the curators determine it is appropriate, they will add the app to that category within one month for existing categories. New categories may take longer if they require updates to the EDAM ontology. 

To request a new or additional category for an app, click to the right of the app name and enter the requested category as a comment. Your suggestion will be emailed to the app integrator and CyVerse app curators.

You can view, rate, and add comments about an app.