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Installing client

Install client

Install client

Diferent clients have different installation steps.

Follow the instructions for your operating system below to install iCommands on your computer.

Add the iRODS repository and install iCommands. Since our servers run iRODS 4.X.Y it is recommended to install version 4.3.X, since there are compatibility issues between icommands 5.0.X and irods 4.X.Y

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# Install required tools if not yet present:
sudo apt-get install wget gpg lsb-release

# Install the (official iRODS) public key and add the repository: 
sudo mkdir -p /etc/apt/keyrings
wget -qO - https://packages.irods.org/irods-signing-key.asc | \
    sudo gpg \
        --no-options \
        --no-default-keyring \
        --no-auto-check-trustdb \
        --homedir /dev/null \
        --no-keyring \
        --import-options import-export \
        --output /etc/apt/keyrings/renci-irods-archive-keyring.pgp \
        --import
echo "deb [signed-by=/etc/apt/keyrings/renci-irods-archive-keyring.pgp 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

# Install:
sudo apt-get install irods-icommands=4.3.4 irods-runtime=4.3.4

# To prevent packages from upgrading do:
sudo apt-mark hold irods-icommands
sudo apt-mark hold irods-runtime

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sudo rpm --import https://packages.irods.org/irods-signing-key.asc
sudo wget -O /etc/yum.repos.d/renci-irods.repo https://packages.irods.org/yum/renci-irods.repo
sudo yum install irods-icommands-4.3.4 irods-runtime-4.3.4

To prevent packages from upgrading edit /etc/yum.conf 
sudo nano /etc/yum.conf

and add below line
exclude=irods-icommands irods-runtime

In Anunna icommands is already installed on the login nodes, you do not need to load a module.

Install iCommands using this guide

There are two ways to install iBridges:

  • As a pyhton dependency. If you know python and would like to see the code, have a look at the github iBridges-GUI repo.

  • As a program. Since release 1.4.0, there is a downloadable zip by operating system. See iBridges-GUI release page.

    • Download it and extract to a folder of your choosing.
    • In macOS: Remove macOS quarantine attributes: 
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      xattr -rd com.apple.quarantine /Users/name/folder/location/ibridgesgui_dist

Release page

In the software center is it available as 'WUR iBridges BETA'.

Release page

Run PowerShell as admin by opening the file location of PowerShell, right clicking on it and selecting 'WUR - Run with administrative rights'.

Note: These installation steps are for users working on windows machines. For installs on other operating systems, please refer to this link.

Now, install GoCMD by copying and pasting the following script: 

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New-Item -ItemType Directory -Path "$env:USERPROFILE\gocmd-irods" | Out-Null ; New-Item -ItemType Directory -Path "$env:USERPROFILE\.irods" | Out-Null ; cd "$env:USERPROFILE\gocmd-irods"
curl -o gocmdv.txt https://raw.githubusercontent.com/cyverse/gocommands/main/VERSION.txt ; $env:GOCMD_VER = (Get-Content gocmdv.txt) ; curl -o gocmd.zip https://github.com/cyverse/gocommands/releases/download/$env:GOCMD_VER/gocmd-$env:GOCMD_VER-windows-amd64.zip ; tar zxvf gocmd.zip ; del gocmd.zip ; del gocmdv.txt ; [Environment]::SetEnvironmentVariable("Path", "$env:Path;$env:USERPROFILE\gocmd-irods", "User") ; exit

This script does the following:

  1. It creates 2 new folders called 'gocmd-irods' and '.irods' in the user profile (C:\Users\abcde001)
  2. Goes into the 'gocmd-irods' folder, installs and unzips gocmd.zip and gocmdv.txt file and cleans up unnecessary zip files.
  3. Adds the folder 'gocmd-irods' to the PATH environment variable and then exits PowerShell.

Given that python 3.9 or later is installed on your machine, open your terminal and install the iRODS client package by running: 

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pip install python-irodsclient

Verify Client Installation

Verify client installation

Diferent client have different installation steps.

After installation you can see if icommands is installed successfully by using this command: 

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ihelp

  • As a pyhton dependency: Start the ibridges-gui from the python scripts folder.
  • As a program: run the executable.

A new window will appear:

Start iBridges

Check if the WUR iBridges is installed. There is a shortcut in the desktop.

Start powerShell again or the normal windows cmd. Then, to check if GoCMD has been installed successfully, run: 

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gocmd --help

N/A (You will be notified through a message in your terminal after the installation.)