Using iCommands to access Yoda

If you work with large amounts of data (up to GB and more, or hundreds to thousands of files), using iRODS iCommands is a better option for handling your data packages. Yoda is based on iRODS technology and using iCommands allows you to interact with the iRODS backend of Yoda directly, transferring data to and from Yoda using the iRODS communication protocol. 

Using iCommands is a significantly faster option than the Yoda Network Disk, but it requires some familiarity with terminals. Therefore, keep in mind that using iCommands may initially take more time compared to connecting via the web portal or the Network Disk. It is suggested that you only use iCommands if you are comfortable with command-line tools. On Windows or MacOS you should also be comfortable setting up and using virtual machines or docker containers, although Windows WSL2 makes it somewhat easier. iBridges or GoCommands are generally considered sufficient for most use cases, and are also considered easier to set up and use. 

In the following instructions, you will need to change the example username to your Yoda username. Your username should contain only lowercase characters.

Version of iCommands matters

Your local iCommands version should match the iRODS version on the Yoda server. This is currently version 4.2.12. 

Installing iCommands

You first need to install client software that supports the iRODS protocol on your PC. Native iRODS iCommands packages are only available on Linux, both for CentOS and Ubuntu. 
 
Windows 10 or Windows 11 users can run the iCommands in the Windows Subsystem for Linux (WSL). We recommend using WSL version 2 (WSL2), since it has fixes for a number of issues in WSL version 1 (WSL1). There are installation instructions in a nutshell: 

  • start PowerShell as administrator 
  • wsl --install -d Ubuntu-18.04 

MacOS users can run the commands inside a Linux VM or Docker container.

Configuring iCommands

You need to configure the iCommands to connect to the right Yoda environment. When running in a virtual machine or docker container you probably also want to ‘map’ your local filesystem locations. 
 
You may find the configuration for your research environment or institution at the end of this section. If not, here are the steps to find your configuration: 

  1. Open Yoda web portal and log in.  
  2. Select your username (on the top right of the screen) 
  3. Go to Data Transfer 
  4. On the Data Transfer page, you can find your configuration information for iCommands.
  5. Select and copy the text including the curly brackets. 
iCommands Configuration

6. Paste this into a file called `irods_environment.json` and place this file in a folder called “irods” in your home directory (so that the full path to the file becomes  ~/.irods/irods_environment.json).

Here are the configurations for Yoda research environments at Utrecht University:

Getting started with iCommands

After installing and configuring the iCommands, you can log in to the Yoda environment using the iinit command. Note that the password you must use for the Network Disk is a data access password.

iCommands to transfer and manage files in sections 5.3, 5.4 and 5.5 of the https://irods.org/uploads/2016/06/irods_beginner_training_2016.pdf iRODS beginner training.

You will find extra information in the iCommands manual here.