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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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Uploading data items

You can upload and import files from your desktop using several different methods:

  • Simple Upload from Desktop is useful if you have smaller files up to 1.9 GB per file.
  • Bulk upload from Desktop uses Cyberduck for bulk upload.
  • Import From URL allows you to paste a URL to the file to upload.
  • Import Genome from CoGe (new for the 2.2. release) allows you to import a CoGe genome within the DE.

Network bandwidth and current load impacts upload times. For more information on larger files and allocations, see Downloading and Uploading Data.

You also can import files from URL that are larger than 3-4 GB or are not on your computer.

Using Simple Upload from Desktop

Simple Upload from Desktop is useful when you have smaller files of up to 1.9 GB per file.

  1. Open the Data window.
  2. In your personal folder, open the destination folder for the upload.
  3. Click Upload and then click Simple Upload from Desktop.
  4. Verify the destination folder (Uploading to) is correct.

     View

    To change the destination folder, click Cancel, select the correct folder, and then click Upload and Simple Upload from Desktop again.

  5. In the Upload window, click Browse to select the first file to upload.
  6. Repeat for each file to upload.
  7. Click Upload. The files are uploaded to the destination folder.

Using Bulk Upload from Desktop

The iDrop Lite Java applet was removed for the 1.9.7 release. We recommend using Cyberduck (for Mac and Windows). LINUX users may want to use iDrop Desktop or iCommands. You also may still upload or import files within the DE using simple upload or import from URL within the DE. The method you use depends on the size and number of your data files, as well as your personal preferences.

You can access and manage data from outside the DE as well. For more information, see Downloading and Uploading Data.

Importing data items

Importing From URL

Use Import From URL when you want to import larger files, have some files you want to upload from desktop and some you want to import from URL, or want to import a file to the DE that isn't on your system.

  1. Copy the URL for the first file to import.
  2. In your personal folder, select the destination folder for the import. (To create a new folder, see Creating a Folder.)
  3. Click Upload and then click Import From URL.

     View

  4. Paste the URL for the file to import in the first row.
  5. Repeat for each file to import.
  6. Click the Import from URL button. The files are imported to the destination folder.
Helpful Links

 On This Page:

Related Pages:

Importing a Genome from CoGe

You can upload a genome directly from CoGe for use in the DE. The genome is imported to the coge_data folder in your personal Data folder.

  1. Open the Data window.
  2. Click Upload and then click Upload Genome from CoGe:

    The organism name, version, chromosome count, and sequence type are displayed. To sort any of the columns, click the column header.
  3. Click to select the genome to upload and then click Import.
    You will receive an email when the genome has completed importing to your coge_data personal Data folder.

Useful information

About status updates

As the import progresses, you receive several status updates in the form of popups, notifications, and emails. Once you have received notification that your file has been successfully imported, it is available in the destination folder.

 If the window isn't updating...

 It may take up to 30 minutes for the window to be updated. Refresh your browser window to see if the changes have taken effect.

Troubleshooting tips

If you experience issues with uploading or importing in the DE, try the following:

  • Check that the file or folder name does not contain special characters. For more information, see Using Special Characters in the DE.
  • If you are using Chrome on Mac OS X, bulk upload may result in Java errors and not launch, due to incompatibility between Chrome and Java. To use bulk upload on Mac OS X, close Chrome and use Safari or Firefox instead.
  • Go to Ask CyVerse and search on upload or import.

For additional assistance, please contact CyVerse Support.

 

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