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i5k Workspace@NAL
U.S. Department of Agriculture

How to upload files to CyVerse

Move your files to the CyVerse Discovery Environment.  

1.     Sign up for a CyVerse account. If you’re not familiar with the CyVerse Discovery Environment (DE), visit the CyVerse wiki for more information.

2.     Log into the Discovery Environment (DE).

3.     Move your data to your CvVerse account. CyVerse recommends using the irods tool for large data transfers.

  • For PC users:

    • The new version of iRODS client does not currently support Windows.
    • CyVerse currently recommends CyberDuck for file transfers

      • There are Windows, OS X and Linux clients available.
      • See the CyVerse support pages for more information on setting up CyberDuck for CyVerse.
    • If you already have the 3.x version, core functionality for uploads should still work:

      • Double-click on irods_exp.exe to launch the program.
      • Under ‘Name’, enter your CyVerse user name; ‘Host’, data.iplantcollaborative.org; ‘Zone’, iplant; ‘Port’, 1247. Enter your password, and click connect.
      • Under ‘Storage Resource’, select ‘homeResc’.
      • To upload data, select the ‘iRODS’ menu item -> Upload -> Upload Files (or folder)
      • Navigate to your file (or folder) and double-click to begin the upload.
      • Note that this may take a while (>1 hour) for large files.

 

  •  For Mac users:

    • Follow the CyVerse instructions for setting up the Mac icommands binaries.
    • Using the command line interface (e.g. Utilities -> Terminal), navigate to the directory where you downloaded icommands (e.g. cd ~/Desktop).
    • Make a directory to store the commands in, e.g. mkdir icommands.
    • Move the tar archive into the new directory: mv irods3.2.icmds.mac.intel.tar icommands
    • Navigate to the icommands folder: cd icommands
    • Untar the icommands tar archive: tar -xvf irods3.2.icmds.mac.intel.tar
    • Type ./iinit
    • Enter the following login information:

      • Host name (DNS) of server to which to connect: data.iplantcollaborative.org
      • Port number:1247
      • iRODS user name: <your CyVerse login name>
      • iRODS zone: iplant
      • Current iRODS password: <your CyVerse password>
    • To upload your data into your CyVerse home directory, type: ./iput –vp <path-to-your-file>
    • Note that this may take a while for large files.

c.     For Linux users:

d.     Alternatively, you can try to use the CyVerse GUI to upload your data. However, this may not work for large files. Log on to your CyVerse DE account. In your ‘Data’ window in the CyVerse DE, go to upload, and select the method with which you would like to upload your data. CyVerse will send you notification messages on the progress of the upload.

 

Share your files.

 

4.     Select each file that you would like to share by clicking on the check-box to the left of the file name. Then, go to ‘Share’ -> via the Discovery Environment, and type ‘NAL Bioinformatics’ in the search box at the bottom. Select this name when it shows up. Under Permissions, select ‘Write’. Click ‘done’.

5.     Send an email to i5k@ars.usda.gov with the following information:

  • The organism name;
  • The path(s) to the shared file(s) on CyVerse (e.g. /username/my_analysis/alignment.bam)