WebDav#

It is possible to use webdav in iRODS by placing the URL that is normally used for the authentication procedure in your web browser. It should prompt a username / password panel which when succesfully will show you the iRODS instance content.

It is also possible to mount the iRODS instance as a network drive. Select the tab that corresponds to your environment for more details.

iCommands#

Currently the latest version of iCommands is only available through a Linux environment. The easiest approach to have icommands available on your system is through Docker.

To install docker look at your operating system below:

Vagrant#

Vagrant is the command line utility for managing the lifecycle of virtual machines. Isolate dependencies and their configuration within a single disposable and consistent environment. Vagrant is distributed as a binary package for all supported platforms and architectures. You can also compile Vagrant from source, which is covered in the README.

Installation#

The documentation for the installation of vagrant is available at: https://developer.hashicorp.com/vagrant/install

macOS package manager#

brew tap hashicorp/tapbrew install hashicorp/tap/hashicorp-vagrant

Windows#

For windows you can download the binary package at: https://developer.hashicorp.com/vagrant/install#windows

Linux#

For linux there are several flavours available at: https://developer.hashicorp.com/vagrant/install#linux However it is very likely that iCommands is directly available for you for your operating system.

Initialize a project directory#

From the documentation at Vagrant…

The first step to configure any Vagrant project is to create a Vagrantfile. The Vagrantfile allows you to:

  • Mark the root directory of your project. Many of the configuration options in Vagrant are relative to this root directory.

  • Describe the kind of machine and resources you need to run your project, as well as what software to install and how you want to access it.

Create a directory

  • Mac/Linux: mkdir vagrant_getting_started

  • Windows: Use file explorer to create a folder

Initialize the project

Make sure you are inside your project folder using the command line interface

vagrant init vagrant init generic/ubuntu2204

A `Vagrantfile` has been placed in this directory. You are now
ready to `vagrant up` your first virtual environment! Please read
the comments in the Vagrantfile as well as documentation on
`vagrantup.com` for more information on using Vagrant.

There are many other vagrant images available but for this documentation we stick to a relatively recent ubuntu 22.04 image. Other images can be found at https://app.vagrantup.com/

Boot an environment

Now that you have initialized your project and configured a box for it to use, it is time to boot your first Vagrant environment.

vagrant up

Bringing machine 'default' up with 'virtualbox' provider...
==> default: Box 'generic/ubuntu2204' could not be found. Attempting to find and install...
    default: Box Provider: virtualbox
    default: Box Version: >= 0
==> default: Loading metadata for box 'generic/ubuntu2204'
    default: URL: <https://vagrantcloud.com/api/v2/vagrant/generic/ubuntu2204>
==> default: Adding box 'generic/ubuntu2204' (v4.3.12) for provider: virtualbox (amd64)
    default: Downloading: <https://vagrantcloud.com/generic/boxes/ubuntu2204/versions/4.3.12/providers/virtualbox/amd64/vagrant.box>
Progress: 3% (Rate: 12.0M/s, Estimated time remaining: 0:03:08)

==> default: Machine booted and ready!

SSH into the machine

You will not actually see anything though, since Vagrant runs the virtual machine without a UI. To prove that it is running, you can SSH into the machine:

vagrant ssh

vagrant@ubuntu2204:~$

Installing iCommands

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
sudo apt-get install irods-icommands

Docker#

To start the docker container with the icommands available you can use this command:

docker run -it --entrypoint /bin/bash docker-registry.wur.nl/m-unlock/docker/irods:latest

As this is a clean docker instance it does not contain any authentication documentation. You can create the required irods_environment.json file inside the docker instance but upon starting a new instance this information is lost.

The best approach would be to exit the docker container and create an irods folder containing the irods_envrionment.json file. There are also additional features within this json file that ensures that your connection is encrypted and that you do not need to provide all access information each time you start the docker container.

  • Create an irods folder

  • Create an irods_environment.json file in the irods folder with the following content

{
    "irods_user_name": "<USERNAME>",
    "irods_zone_name": "unlock",
    "irods_host": "unlock-icat.irods.surfsara.nl",
    "irods_port": 1247,
    "irods_client_server_negotiation": "request_server_negotiation",
    "irods_client_server_policy": "CS_NEG_REQUIRE",
    "irods_encryption_key_size": 32,
    "irods_encryption_salt_size": 8,
    "irods_encryption_num_hash_rounds": 16,
    "irods_encryption_algorithm": "AES-256-CBC",
    "irods_ssl_verify_server": "cert"
 }

Make sure that you change your USERNAME, ZONE and HOSTNAME to the correct values.

When starting the docker container it is essential that the irods folder is mounted to the internal location of ~/irods/. The mounting of the folder is achieved via the -v parameter.

docker run -it -v /PATH/TO/IRODS/FOLDER:/root/.irods docker-registry.wur.nl/m-unlock/docker/irods:latest

When the docker container has succesfully started you can login via the iinit command

> iinit
Enter your current iRODS password:

When that is succcessful the iCommands are available for use. See ihelp or for more information.