Using iBridges to access Yoda

1. Install Python on your computer. You can find installation instructions here. If you already have Python installed, check if it is version 3.8 or higher.
2. Open a terminal program. This can be an Anaconda prompt (if you have installed Anaconda Navigator), a Unix shell, a Powershell, git bash, etc.
3. In the terminal, install iBridges via 'pip', the Python package manager that is automatically installed with Python:
   pip install ibridges

If you work at Utrecht University, there are template configuration files available (if not, please continue to Step 5). To obtain them, open a terminal such as Anaconda prompt, Unix shell, Powershell, git bash, etc. and execute: pip install ibridges-servers-uu.

1. Start the iBridges GUI.
   • If you installed via terminal, type in the terminal: ibridges gui.
   • If you downloaded a pre-built executable, run the executable.
2. From the main menu, click 'Configure' → 'Add Configuration'.
3. If in the dropdown there are templates available, select the relevant template and replace 'EMAIL_ADDRESS' with your email address in the ‘irods_user_name’ field. If no template is available, skip to Step 4.
   
   Click 'Save as', enter a file name, and save it as .json file (e.g., 'irods_environment.json'). Ensure that the folder is '.irods' when saving. When you have saved the file, click 'Check' and, when you get no errors, 'Close'.
4. If in the dropdown menu there are no templates available, click the 'New Config' button to add a new configuration file.
5. You can find the correct values of the required fields for your Yoda instance by going to the Yoda web portal, clicking your username, and selecting  'Data Transfer'. A pre-compiled configuration should be available for inspection, copy, and download. (See also the page: Configuring iCommands)
   
   Click 'Save as', enter a file name, and save it as .json file (e.g., 'irods_environment.json'). Ensure that the folder is '.irods' when saving. When you have saved the file, click 'Check' and, when you get no errors, 'Close'.

• If you work at Utrecht University, you can follow the steps outlined here to configure iBridges.
• If you do not work at Utrecht University, please follow the set-up instructions in this tutorial.

To start using the iBridges GUI, please follow the iBridges instructions to start a new session. Use your Data Access Password as the password to log in. Use the iBridges user documentation to see what you can do with the iBridges GUI.

For use with Python, the iBridges documentation contains multiple interactive Python notebooks to show you the capabilities of the iBridges Python package.

You can immediately start using iBridges in the Command Line Interface (CLI). Simply try executing 
ibridges --help 
or
ibridges <command> --help 
to get examples and help for the usage. For instructions on how to use the iBridges commands, please check the iBridges documentation.