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

DISCOVERY ENVIRONMENT USER MANUAL

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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).

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.

 Wondering why an app you used to use isn't there anymore?

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:
    • 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.

About categories

In the left panel, the Categories are displayed.

  • My Apps: Apps and workflows you are in the process of creating and editing that you have not yet made public, your favorite apps, the apps you have already made public, and the apps that have been shared with you by other users. Click the My Apps tab, click the folder to use, and then click the app to use in the right panel. Note that the category name is displayed above the right panel.
  • Topic: Public apps categorized by science type (such as biology, biomedical science, etc.). Click the Topic tab, navigate through the categories to the correct topic, and then click the app to use in the right panel. The path and category name are displayed above the right panel.
  • Operation: Public apps categorized by operation type (such as alignment, analysis, etc.). Click the Operation tab, navigate through the categories to the correct operation, and then click the app to use in the right panel. The path and category name are displayed above the right panel.
  • HPC: High-performance computing (HPC) apps that may be submitted directly to the Agave API. HPC apps, which are contained in a different repository, require that you sign in to the Agave server the first time you open either the DE, the Apps window, or click the HPC tab. Once you have done so, you will rarely have to authenticate again. Click the HPC tab, authenticate if necessary using your CyVerse username and password, and then click the app to use in the right panel. For more information, see Using HPC Apps in the DE and The Agave API.

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.

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.

  • Private apps (either an app you created and have not yet made public, or a private app that has been shared with you by another user) have a blue lock icon: .
  • Beta apps (Apps that have been made public but have not yet been vetted by our team) have a green Beta icon: .
  • Disabled apps (apps that can no longer be used, most often because they don't work properly) have a red X icon: .
  • Public apps that are not in beta or disabled status have no icon.

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.

 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 support@cyverse.org 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.

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