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How to access the Research Data Storage Service through iRODS

This guide outlines options for accessing the Research Data Storage Service through iRODS

This guide is aimed at...

  • Researchers

Before you start...

Please note that you need to have registered a project with RDS in order to be able to access the storage. If you’d like to do that please read the Research Data Storage Service overview for details.

Most projects on RDS will be assigned to the GPFS facility by default upon registration, this guide is for users who have been given the alternative iRODS/WOS storage. 

The iRODS/WOS storage facility can be accessed via the command line, or via a 3rd-parry graphical user interface. Cyberduck is our preferred (free) interface for iRODS/WOS.

Instructions

There are two methods for accessing the UCL iRODS service:

Cyberduck - graphical client for Windows and OS X

Please see the below Introductory video for assistance with installation and basic usage of Cyberduck on Windows. To access a full high definition version please go directly to the following UCL Media Central link

NB: Cyberduck 5.3.x is incompatible with iRODS.

MediaCentral Widget Placeholderhttp://mediacentral.ucl.ac.uk/Player/7752

 

  1. Download and install Cyberduck (link).
  2. Download and open the UCL RDS Cyberduck profile (right click and select 'save link as' to download). Once saved, double click the downloaded file and Cyberduck will automatically open the profile as a new Cyberduck bookmark. 
  3. Edit the Cyberduck profile…

    Edit the profile as shown, changing Path: to /rdZone/live
     

  4. Close the profile and open the bookmark in Cyberduck

    If the bookmark is not visible, then you can bring it up by going to the menu Bookmark->Toggle Bookmarks

    You will be presented with a login prompt.

    Enter your UCL username and password.
     

  5. Once you have successfully connected you have a view of all the projects of which you are a member.

    In the example below the user is a member of two projects.
     

    The Cyberduck project view…

  6. Subsequent logins only require you to click on the saved bookmark in the Cyberduck window, it is not necessary to use the profile file again.

    Please note that you will not be able to upload any files until the RDS Team have approved your project application and created your project space.

iCommands - command line tools

The iCommands are not installed by default with Linux. However, they are installed on all of our login nodes and can be made available on Legion with the command:

module add icommands

There are too many commands to document fully here; there is full documentation available at the iRODS website. I shall restrict myself to some common commands.

The commands may be downloaded from iRODS download (link). Currently the distributions supported are CentOS, Ubuntu and OpenSuSE. Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods of your home directory (note the dot at the start of the directory name). A template of this file is available: download irods_environment.json. You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your UCL username in the place for irods_user_name

Logging into iRODS

  1. Run the command iinit. This will log you in to the system. If you get asked for extra information such a hostname or port number then check the file irods_environment.json you created before and try again.
  2. iinit asks for your password and creates a session for you which is accessed  when you subsequently use the iCommands. If you wish the session to expire then use the option ttl <time-in-hours> when running iinit. This will expire the session after the configured number of hours.
  3. The command iexit full will log you out of iRODS and require re-authentication by iinit.

Navigating the irods directory tree

  1. The command ipwd shows your current location in the iRODS directory tree. This is analogous to the UNIX command pwd
  2. The command icd changes your location in the iRODS directory tree. This is analogous to the UNIX command cd

Basic copying   of data in and out of iRODS

  1. To copy a file myFile.tar from the current (Unix) directory to the current working directory in iRODS, as discovered by ipwd, use iput myFile.tar
  2. To copy a file myFile.tar from the current (Unix) directory to a named collection in iRODS (/rdZone/live/rd0000/Bob), use iput myFile.tar /rdZone/live/rd0000/Bob
  3. To copy a file myFile.tar from the current iRODS working directory, as discovered by ipwd, to the current UNIX directory, use iget myFile.tar
  4. To copy a file myFile.tar from a named iRODS directory (/rdZone/live/rd0000/Bob) to the current UNIX working directory, use iget /rdZone/live/rd0000/Bob/myFile.tar

All of the above commands may be extended to transferring whole directories by using the -r option to indicate recursive copying.

Deleting data from iRODS

The command for removing data from iRODS is irm. If you want to delete whole directories then use the -r option to indicate recursive deletion.

Related guides & other info

Help & Support

For further help and assistance you can contact Reseach Data Support (email).

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