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

DISCOVERY ENVIRONMENT USER MANUAL

Maintenance: Tues, 28 Jan 2020

ACCESS TO OR USAGE OF THE FOLLOWING SERVICES WILL BE UNAVAILABLE OR DISRUPTED:

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, http://user.cyverse.org, 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
http://www.cyverse.org/maintenance-calendar
Check your local timezone here https://bit.ly/36iVOkX 
 
Please contact support@cyverse.org for any questions, or concerns.

 

 

 

 

 

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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.

Opening the Apps window

Click Apps to open the Apps window.

Understanding app categories

New for the 2.8 release is a recategorization of the Apps catalog. There now are tabs for My Apps, public apps categorized in the Topic and Operation tabs, and the HPC tab, which contains apps based on 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.

For this release, apps that have not 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.

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, so HPC apps now are available in search.

Wondering what's up with the colored app names?

The color of the app name indicates its status:

  • Apps with red names have been disabled and are not current usable.
  • Apps with blue names mean the app is a Beta app. You can still use the app but be aware that it has not yet been vetted by our team.
  • Apps with green names mean the app is a private app, either one you created, or a private app that has been shared with you by another user.

If an app is no longer listed

A number of apps were deprecated from the Apps catalog for the 2.8 release. 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.

It's also possible that you're searching for an HPC app and you haven't authenticated yet to the Agave server. To do so, click the HPC tab, or log out of the DE and back in, then log in when prompted to authenticate to the HPC server.

Selecting a category

When you first open the Apps window, the tab bar for selecting an app in a tab is displayed. Within each tab, you select a category to display its contents in the right panel.  

  • My Apps: Apps and workflows you are in the process of creating and editing and which 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.
  • Topic: Public apps categorized by science type (such as biology, biomedical science, etc.).
  • Operation: Public apps categorized by operation type (such as alignment, analysis, etc.).
  • HPC: High-performance computing (HPC) apps that may be submitted directly to the Agave API. For more information, see The Agave API.

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.  

To select an app using the tabs, click the tab to use (either My Apps, Topic, Operation, or HPC) to view information about it in the right panel:

  • In the My Apps tab, click the app to use in the right panel. Note that the category name is displayed above the right panel.
  • In the Topic and Operation tabs, navigate through the categories to the correct topic or operation, and then click the app to use in the right panel. The path and category name are displayed above the right panel.
  • In the HPC tab, authenticate if necessary using your CyVerse username and password, and then click the app to use in the right panel.

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.

Requesting a new or different category

You can request that an app be added to an existing category or suggest a new category.

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.

Menus

At the top right of each window in the DE are the window icons: .

At the top of the Apps window are the menus for managing apps and workflows, sharing apps you own with collaborators or making the app public, and searching for an app:

Apps menu

Workflow menu

Share menu

Apps search

Enter part of an app name to find the app, workflow, topic, operation, HPC app, or tool to use.

A number of apps were deprecated from the Apps catalog for the 2.8 release. 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). For more information, see Searching for an App or Workflow.

Helpful Links

 On This Page:

Related Pages:

 

Customizing the Apps window view

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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