A 'zone' in iRODS is an independent iRODS system consisting of various servers and clients. A zone can be dedicated to a single user group or several groups can use the same zone. Currently there are five independent zones for the KU Leuven iRODS projects. Based on your project you will be using one of these zones. Since we operate more than one zone, we have different URLs to reach those zones. Throughout this training you will see links like this: https://{YOURZONE}.irods.icts.kuleuven.be to show you these link can work with your zone name. Whenever you see YOURZONE placeholder, please use your zone name there.
You will be provided with your zone name and an URL to access to that in the training session. Also once your iRODS account is activated, you will be notified by an email about how to access to your zone.
For now, we don't have any federated zones. However, we can federate zones in the future to facilitate data transfer between zones.
For your all questions and requests you can send an email to our service desk. The service desk email address is [email protected].
Time to time you can receive a notification email from the email address below to be informed about changes, updates or maintenances with iRODS. Please pay attention to those mails. The mentioned mail address:
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A KU Leuven account (u- or b-account) to access the KU Leuven iRODS zones
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Being a member of a project
If you want to use iRODS' command line client (iCommands), you need to have following:
- A Linux client environment - a linux based operation system and terminal
- Installed iCommands
If you want to use the python programming client (PRC) with a longer password duration (7 days), you need to have following:
- A Linux client environment - a linux based operation system and terminal
- Installed iCommands
- An installed python release
- The Python iRODS Client (PRC)
If you want to use the python programming client (PRC) with its default password duration (60 hours), you need to have following:
- An installed python release
- The Python iRODS Client (PRC)
As a windows user if you don’t already use any virtualisation system to operate Linux you can install Windows Subsystem for Linux (WSL2).
To be able to install WSL 2 on your Windows 10, you need the following:
- Windows 10 May 2020 (2004), Windows 10 May 2019 (1903), or Windows 10 November 2019 (1909) or later
- Hyper-V Virtualization support
Users who are using a system managed by KU Leuven should fulfill these requirements. The requirements can be checked as follows:
To know your Windows version, type ‘winver’ on your search bar and check your version on coming screen. Anyone who cannot see 2004 should look at this link.
The installation of WSL2 will consist of the following steps:
- Enable WSL 2,
- Enable ‘Virtual Machine Platform’,
- Set WSL 2 as default,
- Install a Linux distro.
We will complete all steps by using Power Shell of Windows. However you can do some of the steps by graphical screens as an option. Here you can find all steps:
- Run Windows PowerShell as administrator,
- Type the following to enable WSL:
dism.exe /online /enable-feature /featurename:Microsoft-Windows-Subsystem-Linux /all /norestart
- To enable Virtual Machine Platform on Windows 10 (2004), execute the following command:
dism.exe /online /enable-feature /featurename:VirtualMachinePlatform /all /norestart
- To set WSL 2 as default execute the command below (You might need to restart your PC):
wsl --set-default-version 2
- To install your Linux distribution of choice (Ubuntu 18.04 LTS is recommended to install the following iRODS packages easily) on Windows 10, open the Microsoft Store app, search for it, and click the “Get” button.
- The first time you launch a newly installed Linux distribution, a console window will open and you'll be asked to wait for a minute or two.
- You will then need to create a user account and password for your new Linux distribution. This password will give you ‘sudo’ rights when asked.
- If you see ‘WSLRegisterDistribution Failed with Error:’ or you may find that things don’t work as intended you should restart your system at this point.
After all these steps when you type ‘wsl’ to your Windows PowerShell, you will be directed to your Ubuntu machine mounted on your Windows’ C drive. From now on, you can execute all Linux commands. It is advised to use the home directory instead of your Windows drives. So if you type ‘cd‘ you will be forwarded to your Ubuntu home.
You can also install (optional) the Windows Terminal app, which enables multiple tabs operation, search feature, and custom themes etc.
To be able to work with iCommands, we first need to install it if it has not been installed yet. You can check ls /usr/bin to find iRODS executable commands on the system.
On a linux OS you can use a package manager to install iCommands in the terminal. Instructions for configuring via the appropriate package manager can be found at the link https://packages.irods.org/. You can find the installation instructions for iCommands 4.3.0 for different operating systems below.
Click here for Centos 7
# Installing prerequisites
yum update
yum install wget sudo
# Add the iRODS repository to your package manager (if you haven't done so already)
sudo rpm --import https://packages.irods.org/irods-signing-key.asc
wget -qO - https://packages.irods.org/renci-irods.yum.repo | sudo tee /etc/yum.repos.d/renci-irods.yum.repo
# Installing iCommands
yum install irods-icommands
Click here for Almalinux 8 or Rocky Linux 8
# Installing prerequisites
yum update
yum install wget sudo
# Add the iRODS repository to your package manager (if you haven't done so already)
sudo rpm --import https://packages.irods.org/irods-signing-key.asc
wget -qO - https://packages.irods.org/renci-irods.yum.repo | sudo tee /etc/yum.repos.d/renci-irods.yum.repo
# irods runtime needs to be installed manually because of https://github.com/k3s-io/k3s/issues/5588
yum install irods-runtime
# Installing iCommands
yum install irods-icommands
Click here for Debian 11
# Installing prerequisites
apt-get update
apt-get install wget lsb-release sudo gnupg
# Add the iRODS repository to your package manager (if you haven't done so already)
wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -
echo "deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main" | sudo tee /etc/apt/sources.list.d/renci-irods.list
sudo apt-get update
# Installing iCommands
apt-get install irods-icommands
Click here for Ubuntu 18 or Ubuntu 20
# Installing prerequisites
apt-get update
apt-get install wget lsb-core sudo
# Add the iRODS repository to your package manager (if you haven't done so already)
wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -
echo "deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main" | sudo tee /etc/apt/sources.list.d/renci-irods.list
sudo apt-get update
# Installing iCommands
apt-get install irods-icommands
Click here for Ubuntu 22
# Installing prerequisites
apt-get update
apt-get install gnupg wget sudo
wget http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1f-1ubuntu2_amd64.deb
sudo dpkg -i libssl1.1_1.1.1f-1ubuntu2_amd64.deb
# Add the iRODS repository to your package manager (if you haven't done so already)
wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -
echo "deb [arch=amd64] https://packages.irods.org/apt/ focal main" | sudo tee /etc/apt/sources.list.d/renci-irods.list
sudo apt-get update
# Installing iCommands
apt-get install irods-icommands
If you have trouble installing iCommands, or if you want to install iCommands on a different Linux distribution/version, please contact [email protected].
Here you will learn how to install Miniconda from command line on Ubuntu 18.04. The whole Miniconda installation procedure needs only 3 steps, except creating and activating a conda environment which is explained later.
- To download the latest shell script to Ubuntu 18.04, execute the following command.
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh- To make the Miniconda installation script executable, do the following.
chmod +x Miniconda3-latest-Linux-x86_64.sh- Run the installation script on Ubuntu 18.04 to install Miniconda.
./Miniconda3-latest-Linux-x86_64.sh- During the installation follow the instructions and give answers to questions.
- Be sure that if you choose ‘yes’ to ‘conda init’ question at the end it will add the base environment to your.bashrc file on your Ubuntu system. But it will not hurt anything.
To install with pip:
pip install python-irodsclientInstead of installing the PRC via pip, you can do it by conda using the environment.yml file. Copy this file to your project directory and update the last part, 'prefix' to your conda environments. And lastly execute the command below.
conda env create --file environment.ymlYou can activate your environment executing the command below.
conda activate prc-irods| Module | Description | Notes |
|---|---|---|
| 02_Introduction_to_iRODS.pdf | Explains all information about iRODS in general as well as the KU Leuven iRODS architecture in particular. Also it contains some hands-on part with logging a hands-on tutorial on how to log in to the KU Leuven portal | This module is valid for users of all available zones |
| 03_ManGO_Portal_Handson_User-Training.md | Contains a guide for the graphical user interface to ManGO, the ManGO portal | This module is mostly for the users that use a portal based GUI client |
| 04_WebDav_Handson.md | Explains the WebDav interface, which provides local filesytem type access to data and teaches you how to use it | This module is mostly for the users and zones that use a desktop based GUI client |
| 05_iCommands_Handson_User-Training.md | Explains how to use the command line client of iRODS | This module is mostly for the users and zones that work with command line interface - terminal |
| 06_PRC_Handson_User-Training.md | Explains how to use the programming client - the Python iRODS client (PRC) to iRODS | This module is mostly for the users and zones that want to interact with python |
| 07_Cyberduck_Handson.md | Explains how to download and configure cyberduck client and teaches how to use it | This module is mostly for the users and zones that want to use a desktop application to interact with iRODS |
| /img (folder) | Place for images of the tutorials | |
| /data (folder) | Place for data objects (files) | will be used in the PRC |
| /miscellaneous (folder) | Place for supporting documentation. It keeps a jupyter notebook for PRC training, some practical information about permission management etc. | useful for the PRC, iCommands and ManGO portal clients |
| environment.yml | Contains a list of dependencies to install | for the users who want to use PRC |
| README.md | Explains the goals and structure of this training repository |
- Click the 'issues' tab at the top of this GitHub page to let us know about your findings or requests.
OR
- Send an email to [email protected]
- Fork this repo to your GitHub account.
- Edits may be made to the fork via the Github web interface or you can clone the repo to work on your local computer. For very significant changes we suggest making a new branch.
- Commit your changes; if working from a local copy, push those changes to your fork in Github.
- Submit a pull request back to the master repository; you may need to act on feedback before your request is merged.