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Data Store FAQ

Managing data

What if I need more space (storage) in the Data Store

Typically, every user has a 100GB allocation in the Data Store. You can request more space by completing an Allocation Increase Form.

Sharing data

How do I publish a large set of public data?

If you need assistance transferring a large dataset to CyVerse, please contact CyVerse Support (support@cyverse.org or use the blue Intercom icon Intercom at the bottom right). For more information on our policies, see CyVerse’s Collaboration Policy and Data Management Policy. For more information on using data at CyVerse, see the Data Store Guide.

What public datasets are in CyVerse?

CyVerse provides web access to its public datasets. Because the CyVerse Data Store underlies all CyVerse services, the public datasets may also be accessed through the Discovery Environment, Atmosphere, the Science APIs and iCommands. For more information on using data at CyVerse, see the Data Store Guide.

How do I request a Community Released Data Folder?

Community Released Data folders are available for evolving datasets that individuals or communities want to make available as quickly as possible for research and reuse, especially within CyVerse analysis platforms. Community Released Data folders are intended for datasets that are growing or changing frequently or that may not need long-term preservation.

Before you request a folder, please read this wiki article Publishing Data through the Data Commons, and this one Preparing Community Released Data Folders.

Then, if you meet the criteria, you can request a folder using this Request for Community Released Data Folders Form.

How do I connect to a shared or public folder with CyberDuck?

If you follow the default configuration for Cyberduck you will automatically be connected to your home directory (/iplant/home/$your_user_name). However, you can also open a new connection to any directory to which you have access permission. This includes folders that other users have shared with you, or public folder, such as those under /iplant/home/shared.

To do this read the instructions below:

Expand to read more

Open a connection to a public folder

  1. Open CyberDuck
  2. If the browser is not already open, select File - New Browser
  3. Create a new connection by clicking on the + in the lower right
    (next to the pencil and minus sign)
  4. In the top dropdown menu, select iPlant Data Store
  5. In the dialog box, name your connection something relevant, like the name
    of the folder you want to browse to
  6. Enter your user name in the appropriate field. If you are connecting to
    public folder, you can also enter anonymous in this field
  7. In the Path field, enter /iplant/home/shared, or some subdirectory.
  8. Close the dialog window. Now, in your list of connections, you should see
    a new connection with the name you chose. Click on that, and you should go
    directly to the public folder.

Once you are connected to /iplant/home/shared, you can browse down to any sub-directory.

Warning

DO NOT try to browse up to /iplant/home/ because it contains >50,000 folders
(one for each CyVerse user) and it will hang up.

Open a connection to a private folder that is shared with you

Follow the same steps as above, except in step 7, enter the path to the folder that was shared with you. For example, if user “janedoe” shares a folder called “data” with you, enter /iplant/home/janedoe/data in the Path field. You cannot connect as anonymous in this case, and must supply your own user name. See also: Cyberduck documentation.

How do I make a folder public with iCommands?

Although you can share files and folders in the DE and create public links, you must use iCommands make them visible to everyone. Permissions are set in iCommands by using ichmod (https://docs.irods.org/4.2.1/icommands/user/#ichmod).

To make a folder public, you give read permission to two users: ‘public’ (anyone signed in with a CyVerse account) and ‘anonymous’ (anyone on the web - no sign in required).

To recursively make a shared folder called ‘myfolder’ public, use the instructions below

Expand to read more

ichmod -r read public /iplant/home/shared/myfolder
ichmod -r read anonymous /iplant/home/shared/myfolder

To remove public access to the folder, use:

ichmod -r null public /iplant/home/shared/myfolder
ichmod -r null anonymous /iplant/home/shared/myfolder

See also our iCommands documentation.

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