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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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Discovery Environment tools are Docker images from which apps are created. There are numerous tools already available in the DE for new apps you are creating. It's easiest to just use one of those tools. However, sometimes the tool or version isn't available, so you can request installation of a new tool or create a new one yourself. If you create a new tool, it is available by default in your personal Tools list and available only for your use. You can share the tool with specific collaborators, or make it public (all tools created prior to the 2.13 release in June 2017 are public).

You can edit and delete a tool you own, as well as jump-start the creation of a new app from the Tools window.

Managing Tools

Adding a tool and Requesting a tool

Editing a tool

For tools you created, you can edit the tool name, description, version, and Docker Hub URL. The image name and tag are not editable after the tool has been created.

  1. In the Apps window, click Manage Tools at the top.
  2. Click to select the tool you own that you want to edit.
  3. Click the Tools menu and then click Edit.
  4. Change the image name, description of the tool, version, and/or Docker Hub URL as needed.
  5. When done, click OK.

Deleting a tool

You can delete a tool you created.

  1. In the Apps window, click Manage Tools at the top.
  2. Click to select the tool you own that you want to delete.
  3. Click the Tools menu and then click Delete.
  4. Click Yes to verify you want to delete the tool.

Using a tool to create an app

Once you've found the tool to use in an app you want to create, you can "jump-start" the creation of a new app right from the Tools menu.

  1. In the Apps window, click Manage Tools at the top.
  2. Click to select the tool to use for the new app.
  3. Click the Tools menu and then click Use in app. The Create App window opens with the tool selected.
  4. Continue to Creating a New App Interface for instructions on how to create the new app.

Sharing tools

Once you have created a tool, by default, it is private and available only for your personal use. You can share it with selected collaborators or make the tool public (the default for all tools created prior to the 2.13 release). You also can edit and delete a tool you created that is in Own status. Giving Own access allows the collaborator to share, edit, and delete the tool, so grant this permission with care.

 Before a new app can be created, the tool that app is based on must be made available in the DE.

Sharing a tool with a collaborator

  1. In the Apps window, click Manage Tools at the top.
  2. Click to select the tool you own that you want to share.
  3. Click the Share menu and then click Share with collaborators.
  4. Select a user in your Collaborators list: Click Choose Collaborators, select the user, click OK, and then click Done.
    To add a new collaborator, click in the search field, begin entering the user's name, and then click the user's name from the list.
  5. To change the collaborator's permission level, click the Permissions down arrow and change the permission.
  6. Repeat for each collaborator.
  7. Click Done.

Sharing a tool with the public

  1. In the Apps window, click Manage Tools at the top.
  2. Click to select the tool you own that you want to share with the public.
  3. Click the Share menu and then click Make public.
  4. This opens a form which you will need to fill it up and click Submit
  5. You will receive email notifications as the tool progresses through the process of making it public.

Unsharing a tool

  1. In the Apps window, click Manage Tools at the top and then click to select the tool to unshare.
  2. Click the Share menu and then click Share with collaborators.
  3. Find the collaborator and click
  4. Click to the right of the collaborator's name.
  5. Click Done.
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