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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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This is the working copy for the 1.4 version of Uploading, Importing, and Downloading Files. At 1.4 release, copy this content over to the main page.

About Uploading, Importing, and Downloading Data Files

This page contains:

You can upload single files, multiple files, and folders from your desktop; import single or multiple files from URL; and download single and multiple files and folders. Once imported, you can use the data files for analyses in the Discovery Environment, as well as manage the data outside of the Discovery Environment using other tools.

  • You can upload files from your desktop using two different methods:
    • For larger files (up to 4 GB) or multiple files or folders, use the iDrop Lite applet.
    • For smaller files (up to 1.9 GB) or if uploading one file at a time, use simple download.
  • You can import files from URL. This is useful for files that are larger than 3-4 GB or when the file is not on your system.
  • You also can upload files directly using iCommands.

The method you use depends on the size and number of your data files, as well as your personal preferences.

Method

< 1.9 GB

< 4 GB*

Single File

Multiple Files

Folders

Requires Java

Upload – iDrop

Upload – Simple

 

 

 

 

Import from URL

 

 

Download – iDrop

Download – Simple

 

 

 

 

* Depending on network bandwidth and current load. See Storing Your Data with iPlant and Accessing that Data for information on larger files and allocation.

Importing and uploading data files and folders

You can upload or folders from your desktop, using either bulk upload or simple upload:

  • Bulk upload uses the iDrop Lite Java applet so that you can upload larger files of up to 4.0 GB each.
  • Simple upload allows you to upload up to four files with a total of 1.9 GB of data.

You also can import files and folders from URL.

The method you choose depends on your personal preferences, the size of the files, and the number of files.

Doing a bulk upload from desktop

This method uses the iDrop Lite Java applet within the Discovery Environment. We recommend using Java version 6 (version 6 update x). For information on using iDrop Desktop, see Using iDrop.

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If you experience difficulties using this method, you may want to see which version of Java you are running.

  1. Open the Data window.
  2. Click the folder from which you want to upload the data files. (To create a new folder, see Creating a Folder.)
  3. Click the Import icon at the top of the window and then click Bulk Upload from Desktop:

  1. If prompted to allow or deny an applet, click Allow.
  2. Navigate to the folder in the Local File System list that contains the files to upload.
  3. Select the files to upload (#1).
  4. Click the >> button (#2).
  5. Verify the upload folder in the Import to section, or click Change Import Location to select a different import folder (#3).
  6. Click Begin Import (#4).
  7. When the iDrop Transfer Completed message is displayed, click OK.
  8. To upload more files, click Clear and repeat.
  9. When done, close the window and click Yes to the confirmation prompt.

As the upload progresses, you receive several status updates. For more information on notifications, see Receiving Notifications.

Once you have received notification that your file has been successfully imported, it is available in the specified folder. If it does not show in your Data folder, click the Refresh icon at the top of the window:

Uploading smaller files

This method is useful if you have smaller files up to 1.9 GB or just want to upload or import one file at a time.

  1. In the Data window, select the target folder.
  2. Click the Upload from desktop icon at the top of the window:
  3. In the Upload window, click Switch to Simple Upload Form at the top left of the window and then click Yes to confirm closing the window and open the simple upload window:
  4. Browse to select the first file to upload from your desktop in the top section or enter the URL for the file to import in the bottom section.
  5. Repeat for each file to upload or import.
  6. Click Upload.

Importing data files from URL

This method is useful when you want to import larger files, have some files you want to upload and some you want to import from URL, or the file isn't on your system.

  1. In the Data window, click your folder.
  2. Click the Import from URL icon at the top of the window:
  3. Copy and paste the URL for the first data file to import:
    (click to enlarge)
  4. Repeat for each file to import.
  5. Click Upload.

As the import progresses, you receive several status updates in the form of popups, notifications, and emails. For more information on notifications, see Receiving Notifications.

Once you have received notification that your file has been successfully imported, it is available in the specified folder.

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If the imported file does not show in your Data folder, click the Refresh icon:

Downloading data files and folders

As with uploading a file, you can download large data files or folders using the iDrop Lite applet, or download small or single files using Simple Download.

Downloading large files or multiple files or folders

  1. In the Data window, select the data files or folders to download.
  2. Click Download at the top right side of the window under Actions (#2).
  3. If prompted to allow or deny an application, click Allow.
  4. Browse to the directory to which you want to download the file and click Choose (#3).
  5. Click Begin Download (#4).
  6. When the download is complete, click OK to close the iDrop Message and then close the Download window.

Downloading small files or single files

  1. In the Data window, select the data file or files to download.
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    You can select more than one file to download, but each file is downloaded separately with this method.

  2. Click Download at the top right side of the window under Actions.
  3. If prompted to allow or deny an application, click Allow.
  4. Click Switch to Simple Download Links at the top left of the window.
  5. Click Yes to close the window.
  6. Click the file to download:
  7. Browse to the download directory and click Save.
  8. Repeat for each file to download.
  9. When done, close the window.
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