Anaconda | Maikel P.H. Verouden, Ph.D.

Anaconda (re-)installation on macOS

Mon, 07 Nov 2022 00:00:00 +0000

Table of Contents

Motivation

Whether working, or studying, everybody uses various sorts and types of software on their computer. Around 34 courses at Wageningen University & Research use Anaconda Python as software in their course, e.g., SSB30806 Modelling in Systems Biology, and SSB32806 Introduction to Systems and Synthetic Biology.

The instructions in this post will show how to install Anaconda on a desktop or laptop computer running macOS as operating system.

In the text some symbol combinations are used for shortcuts, the following table explains the meaning of these symbols in relation to specific keys on your keyboard. To use the shortcuts press the keyboard keys simultaneously, e.g. ⇧⌘A means ⇧+⌘+A.

Icon	Keyboard Meaning	Icon	Keyboard Meaning
⌘	command	⇪	caps lock
⌥	option (or alt)	↩	carriage return (return/enter)
⌃	control	⌫	delete/backspace
fn	function	⌦	forward delete (fn + ⌫)
⇧	shift (either left or right)	⎋	escape

Complete removal of a previous Anaconda installation on macOS

If you have previously installed Anaconda and wish to re-install the latest version or your current installation is not working as you expect, you first need to delete everything related to Anaconda. In macOS a complete removal is somewhat complicated, but doable if you follow all steps precisely as provided in this post.

For the complete removal of everything related to Anaconda the Terminal application will be used. In your Finder > Applications (shortcut: ⇧⌘A) there is a Utilities folder as depicted in Figure 1 below.

Finder Utilities Folder.

Within this Utilities folder, which can be directly accessed by using the ⇧⌘U shortcut, the Terminal application is contained. The icon in Figure 2 shows what the Terminal application looks like in the Finder > Applications > Utilities folder.

Icon Terminal Application.

The Terminal application can also be started via Lauchpad under the ‘Other’ group.

Steps for a complete removal of Anaconda on macOS:

Start the Terminal application. The terminal console prompt, where the commands will be entered, is depicted by a % or a $ sign. Which sign is shown, depends whether your default shell is zsh (% sign) or bash ($ sign).
Install the anaconda-clean package:
```
conda install anaconda-clean
```
Then, run anaconda-clean with the argument --yes to remove all those files and directories without being asked to confirm each one:
```
anaconda-clean --yes
```

anaconda-clean --yes creates a backup of all files and directories that might be removed in a folder named .anaconda_backup in your home directory. Also note that anaconda-clean leaves your data files in the AnacondaProjects directory untouched.

Remove all Anaconda directories from your system by sequentially executing the following commands:

rm -rf /Applications/Anaconda-Navigator.app
sudo rm -rf /opt/anaconda3
rm -rf ~/.anaconda_backup

Sequentially open .bash_profile, tcshrc, .xonshrc, and .zshrc in TextEdit and delete the section starting with # >>> conda initialize >>> and ending with # <<< conda initialize <<<.

In a terminal this is done, e.g. for .bash_profile, with open -a TextEdit .bash_profile. Use the shortcut ⌘S to save the file, and close the file with the shortcut ⌘Q.

Having performed all 5 steps given above, your mac will be ready for a new installation of Anaconda.

Download

At the time this post was written, the latest release of Anaconda was version 2022.10 containing Python 3.9.13. It has been updated to the latest release version 2025.06-1 of Anaconda containing Python 3.13.5.

For newer versions of Anaconda than 2022.10 the steps described below are the same and still correct, but start with a newer version of the downloaded installer package file of Anaconda. The screenshots in this post have not been updated. Therefore, what you see during your installation can (and probably will) differ with respect to the version number shown in the screenshots.

For macOS there are two downloads of Anaconda available on the Anaconda Repository Archive. To see which version you need click on in the menu bar and select ‘About This Mac’.

NOTE: If you are using a mac with the newest M1, M2 or M3 processor, download the Apple Silicon arm64 build!

Download Anaconda for your specific version of macOS using one of the following links:

For an Intel processor based mac: Anaconda3 2025.06-1 (ca. 800.3 MB, Intel 64-bit build)
For a M1/M2/M3/M4 processor based mac: Anaconda3 2025.06-1 (ca. 781.3 MB, ARM 64-bit build)

Installation

For installing Anaconda on macOS follow these steps:

Open the downloaded file, either Anaconda3-2025.06-1-MacOSX-x86_64.pkg, or Anaconda3-2025.06-1-MacOSX-arm64.pkg depending on the processor in your mac (as explained above). This file will most likely reside in Finder > Downloads (shortcut: ⌥⌘L). The file can more easily be found by switching into List view (shortcut: ⌘2). To switch to Icon view use the shortcut: ⌘1.
The installler will start by displaying a message as shown in Figure 3. Click ‘Allow’ to let the package determine if the software can be installed.

Determine whether package can be installed.

When the package can be installed the welcome screen of the Anaconda3 Installer will be displayed as shown in Figure 4. Click the ‘Continue’ button to proceed with the installation.

Welcome Anaconda3 Installer.

Now the Read Me for the software to be installed as displayed in Figure 5 below. Click the ‘Continue’ button to proceed.

Anaconda3 Installer Read Me.

Right after the Read Me a Software Licence Agreement will appear as shown in Figure 6. By clicking the ‘Continue’ button you will be asked to agree with this software licence agreement as diplayed below in Figure 7. Click on ‘Agree’ to proceed.

Aanconda3 Software License Agreement.

Agree to Software License Agreement.

The installer will let you select how you want to install the software as shown in Figure 8. It is recommended to leave the settings as provided and click the ‘Continue’ button.

Select the installation type.

After selecting the installation type the installer asks to provide an installation destination as displayed in Figure 9. Also here it is recommended to leave the default settings and click the ‘Install’ button.

Select the installation location.

Your system will ask to either provide the password (see Figure 10) or use the fingerprint scanner to confirm the software installation.

Confirm the software installation.

Your system may ask you to allow access to your Downloads folder, as shown in Figure 11. Click the ‘OK’ button to grant access to the Downloads folder.

Allow access to the Downloads folder.

Once the files have been installed the Anaconda3 installer will display a message about DataSpell as shown in Figure 12. If your interested visit [https://www.anaconda.com/dataspell]. To proceed with the installer click the ‘Continue’ button.

Message about DataSpell.

After the DataSpell message the Anaconda3 installer has reached the end (see Figure 13). Click on the ‘Close’ button to finalize the installer and close the installer.

Finish and close the Anaconda3 installer.

Congratulations 😆, you now have Anaconda3 2025.06-1 containing Python 3.13.5 installed on your mac!

Before actively using Anaconda, some configuration may be required. The configuration is described in the next section.

Configuration Anaconda3

Upgrading Anaconda Navigator (Anaconda3)

When starting Anaconda Navigator from your Applications folder, the Navigator may open displaying the message shown in Figure 14.

Upgrade available for Anaconda Navigator

To upgrade Anaconda Navigator follow these steps:

Click on ‘Yes’ as shown in Figure 14.
Continue the procedure as indicated on your display to perform the update of Anaconda Navigator.

Add a R kernel

After installing Anaconda3 only the Python kernel is present. To add a R kernel for use inside Jupyter Notebook or JupyterLab perform the following steps:

Open the Terminal application as described above in Complete removal of a previous Anaconda installation on macOS.
Start R by typing R and press return ↩ to execute.
Add the R prompt type the following commands sequentially and after each command press return ↩ to execute. Below version 4.2.1 of R is assumed, do not forget to change the R version number when you are using a different version of R!
```
 ## At the R prompt, indicated by >
 install.packages("IRkernel")
 IRkernel::installspec()
 q()
 # Question in R: Save workspace image? [y/n/c]: n
```
Close the Terminal application by typing exit and press return ↩ to execute.

Now the R kernel will be available in Jupyter Notebook and JupyterLab.

Add a Julia kernel

After installing Anaconda3 only the Python kernel is present, unless you already have added a R kernel. To add a Julia kernel for use inside Jupyter Notebook or JupyterLab perform the following steps:

Open the Terminal application as described above in Complete removal of a previous Anaconda installation on macOS.
Start Julia by typing julia at the terminal prompt and press return ↩ to execute. Once Julia has started, you will see the prompt displayed as julia>.
Type ] and the prompt will change into (@v1.8) pkg>. This under the assumption that you have Julia v1.8.2 or later installed. For other versions of Julia the version number for package management will differ.
Type the command add IJulia and press return ↩ to execute. This will install a lot of packages and make the Julia kernel available in Jupyter Notebook and JupyterLab.
Close the Julia package manager by pressing the BACKSPACE key on your keyboard.
Type exit() and press return ↩ to execute, in order to close Julia.
Close the Terminal application by typing exit and press return ↩ to execute.

Now the Julia kernel will be available in Jupyter Notebook and JupyterLab.

Anaconda installation on Windows 10/11

Sun, 06 Nov 2022 00:00:00 +0000

Table of Contents

Motivation

This post will show how to install Anaconda Python (Anaconda3) on a privately owned desktop or laptop computer running Windows 10 or Windows 11 as operating system.

The installation instructions in this post are not to be used on WURclient desktops or laptops! For a WURclient desktop or laptop see the post: Custom Anaconda installation on a WURclient compute.

Two ways to install Anaconda are offered here:

WUR AppStore. This is the RECOMMENDED way!
Manual installation for those who, for whatever reason, do not want to use the WUR AppStore.

1. WUR AppStore

The WUR AppStore is the place where you will be able to download, link to, or virtually access the software you need for your study programme and courses. Not only during the computer labs and courses, but also for self-study after those.

For more information see: What is the WUR AppStore

Windows 10/11 compatibility and WUR AppStore installation

To safely use the study and course software, you need to connect your laptop to the WUR network with your WUR account. Windows 10 or 11 Education Edition or Professional Edition is needed on your laptop to be able to access the WUR AppStore. If you are using a Home Edition of Windows 10 or 11, you will be automatically upgraded to the Education Edition.
If you have Windows 10 or 11, you can proceed to the manual: How to connect to the WUR AppStore.

Using the WUR AppStore

The use of the WUR AppStore is very well described by the WUR TEAM Study Anytime, Anyplace. The first article can be found here: How can I use the WUR AppStore

The WUR AppStore currently contains Anaconda3 2025.06-0.

Support WUR AppStore

In case you need support installing or using the WUR AppStore you can contact the WUR Servicedesk IT either by telephone: +31 (0)317 488888 / mail: Servicedesk.IT AT wur.nl. You can also visit the Servicepoint IT, ground floor left of the Grand Café, in Forum (Building 102) on the WUR Campus.

2. Manual Installation

By default the Anaconda installer wants to install into the C:\ProgramData folder of your Windows Operating System. According to Microsoft this folder is “used by applications to store data for standard users, because it does not require elevated permissions”. However, it is not recommended to use for installing software. The reason, the Anaconda installer chooses this folder, is that it does not contain a whitespace character like in C:\Program Files\. The Anaconda software can not deal with whitespace characters in path names, while running.

To prepare the Anaconda installation a folder needs to be created prior to the installation of Anaconda. Either create the folder C:\MyPrograms yourself in File Explorer, or perform the following steps exactly as described:

Search for the Command Prompt App by typing cmd in the search field of the Windows task bar. Press return (Enter) to start the application. A window will appear similar to as displayed in Figure 1 showing your own system username.

Windows Command Prompt Application window

Create the directory C:\MyPrograms. This is done by copying (CTRL+C) the following line, pasting (CTRL+V) it behind the prompt and pressing return (Enter) to execute. In case the directory already exists, the message A subdirectory or file C:\MyPrograms already exists. will appear.

mkdir C:\MyPrograms

The Command Prompt application can now be closed by typing exit and executing it by pressing return (Enter).

Download

At the time this post was written, the latest release of Anaconda3 was version 2022.10. It has been updated to the latest release version 2025.06-1 of Anaconda3.

The installer for Windows 10/11 can be downloaded directly from this link: Anaconda3 2025.06-1 for Windows (ca. 914.6 MB, 64-bit).

From Anaconda3 version 2022.10 the installer is only available for 64-bit Windows 10/11 and will not install on a 32-bit version of the Operating System.

Installation

For newer versions of Anaconda3 than 2022.10 the steps described below are the same and still correct, but start with a newer version of the downloaded executable installer file of Anaconda3. The screenshots in this post have not been updated. Therefore, what you see during your installation will differ with respect to the version number shown in the screenshots.

Right-click the downloaded file Anaconda3-2025.06-1-Windows-x86_64.exe and select ‘Run as administrator’, as shown in Figure 2. This file will most likely reside in your Downloads folder of your user account.

Start Anaconda Installer as administrator

Windows will ask for permission to allow the application to make changes to your device as shown in Figure 3. Click ‘Yes’ to continue.

Permission request for changes.

After the installer has started, a first selection window will appear as displayed below in Figure 4. Click the ‘Next >’ button to proceed.

Welcome to Anaconda3 2022.10 (64-bit) Setup.

The installer will now display the license agreement for installation of Anaconda3, as shown below in Figure 5. Click on the ‘I Agree’ button to agree to the terms.

Anaconda3 Setup License Agreement

After agreeing to the license terms, the Anaconda3 setup will ask for whom you wish to install for, as displayed in Figure 6. Select the radio button ‘All Users (requires admin priveleges)’ and click on the ‘Next >’ button to proceed.

Anaconda3 Setup Select Installation Type

Having selected the installation type, the Anaconda3 setup will request for an installation location as shown in Figure 7. Change the destination location to C:\MyPrograms\Anaconda3, to match Figure 7, by typing the destination path directly into the text field displayed (currently showing C:\ProgramData\Anaconda3). Click on the ‘Next >’ button to continue.

Anaconda3 Setup Choose Installation Location

After selecting the installation location folder the Advanced Installation Options will appear, as displayed below in Figure 8. Leave the selection as displayed and click on the ‘Install’ button to start the installation.

Anaconda3 Setup Advanced Installation Options

Once the installation has been completed Figure 9 will be displayed. Click on the ‘Next >’ button to continue.

Anaconda3 Setup Installation was completed successfully

Next the Anaconda3 Setup will show some information on how great Anaconda works with DataSpell, as shown in Figure 10. Click the ‘Next >’ button to proceed.

Anacond3 Setup message about Anaconda and DataSpell

Finally the Annaconda 3 Setup shows that installation has been completed as displayed in Figure 11. Remove the tick marks from the boxes in front of ‘Anaconda Distribution Tutorial’ and ‘Getting Started with Anaconda’, unless you want to display this information, click the ‘Finish’ button to finish off the installation and close the Anaconda3 Setup.

Completing Anacond3 Setup

Congratulations, 😆, you now have Anaconda3 version 2025.06-1 containing Python 3.13.5 installed on your Windows desktop or laptop computer!

Below in Configuration Anaconda3 you find information about additional tasks you may need to perform.

Use the ones required!

Configuration Anaconda3

Upgrading Anaconda Navigator (Anaconda3)

When starting Anaconda Navigator from your Start Menu the Navigator may open displaying the message shown in Figure 12.

Upgrade available for Anaconda Navigator

To upgrade Anaconda Navigator follow these steps:

Click on ‘Yes’ as shown in Figure 12.
Windows will ask for permission to allow the application to make changes to your device as shown in Figure 13. Click ‘Yes’ to continue.

Permission request for changes to update.

Continue the procedure as indicated on your display to perform the update of Anaconda Navigator.

Add a R kernel

After installing Anaconda3 only the Python kernel is present. To add a R kernel for use inside Jupyter Notebook or JupyterLab perform the following steps:

Open the Start Menu and navigate to ‘Anaconda3 (64-bit)’.
Start ‘Anaconda Powershell Prompt (Anaconda3)’. A window will open displaying the prompt as (base) PS C:\>.

Navigate to where R.exe is located. Let’s assume you have R v4.2.1 installed, either via the WUR AppStore or via R installation on Windows 10/11. For other R versions than 4.2.1 do not forget to change the R version number!

Use the following commands:

 cd C:\Program Files\R\R-4.2.1\bin\
 .\R.exe
 ## At the R prompt, indicated by >
 install.packages("IRkernel")
 IRkernel::installspec()
 q()
 # Question in R: Save workspace image? [y/n/c]: n
 ## back at the powershell prompt, indicated by (base) PS C:\>
 exit

Now the R kernel will be available in Jupyter Notebook and JupyterLab.

Add a Julia kernel

After installing Anaconda3 only the Python kernel is present, unless you already did Add a R kernel . To add a Julia kernel for use inside Jupyter Notebook or JupyterLab perform the following steps:

Open Julia on your WURclient. A window will open and you will see the prompt displayed as julia>
Type ] and the prompt will change into (@v1.8) pkg>. This under the assumption that you have Julia v1.8.2 or later installed. For other versions of Julia the version number for package management will differ.
Type the command add IJulia. This will install a lot of packages and make the Julia kernel available in Jupyter Notebook and JupyterLab.
Close the Julia package manager by pressing the BACKSPACE key on your keyboard.
Type exit() to close Julia.

Now the Julia kernel will be available in Jupyter Notebook and JupyterLab.

Custom Anaconda installation on a WURclient computer

Thu, 03 Nov 2022 00:00:00 +0000

Table of Contents

Motivation

A WURclient desktop or laptop at Wageningen University & Research is not a standard Windows 11 computer. WURclients use Windows 11 Enterprise, which has been modified by Facilities and Services Information Technology (FB-IT) among others with respect to installation rights for security reasons.

Classic WURclient desktops and laptops at Wageningen University & Research can install RStudio from the Software Center created by the IT department, which is launched by clicking on Start and selecting the “Software Center” tile. Modern WURclient desktops and laptops use the “WURAppStore” instead. The available version of Anaconda Python (Anaconda3) in Software Center is Anaconda Python 2025.06-0, whereas in the WURAppStore it is named Anaconda3 2025.06-0.

This version of Anaconda Python was packaged for educational purposes. Only once per year a new version of Anaconda Python is released in Software Center (for Classic WURclients) and WURAppStore (for Modern WURclients, and course software for students).

Many users, however, would like to use a newer version of Anaconda Python than the one in Software Center. At the moment of writing this post the latest version of Anaconda Python released on the Anaconda Repository Archive is Anaconda3 version 2022.10 containing Python 3.9.13 (released on 2022-10-17). The post has been updated, with the exception of the screenshots, to Anaconda3 version 2025.06-1 containing Python 3.13.5 (released 2025-07-18).

This post will show how to custom install Anaconda Python on a WURclient desktop or laptop computer without using Software Center.

The installation instructions in this post are not to be used on privately owned desktops or laptops! For a privately owned desktop or laptop see the post: Anaconda installation on Windows 10/11.

Prerequisite

To be able to perform a custom installation of R you need to have POWER USER RIGHTS on the WURclient desktop or laptop.

To see whether you possess these rights, right-click any icon (except Recycle Bin or WUR HELP) on the desktop. When the opened menu contains the option ‘WUR - Run with administrative rights’ (seventh or eighth from the top), it means you have power user rights on that particular desktop or laptop.

Uninstall a previously installed Anaconda Python version

Before performing a new custom installation of Anaconda it is recommended to uninstall a previously installed version.

Here two procedures are described, follow the one that fits your needs:

In case you have no version of Anaconda installed on your WURclient desktop or laptop you can proceed to the section Custom Anaconda installation.

Installed from Software Center

If you previously installed Anaconda Python from Software Center, then to remove Anaconda Python reopen the Software Center by clicking on Start and next click on the Software Center tile. If for some reason you lack this tile in your start menu, just type ‘Software Center’ and it will appear in a search results window in your Windows task bar.

In the left column of Software Center navigate to “Installation Status”. Select the installed Anaconda Python version and click on the green button bearing the text “Uninstall”. This will start the removal of the software. You will be informed by the Software Center, when the software has been uninstalled.

If you have not installed another version of Anaconda Python, either via Software Center or via a custom installation, your computer should now be lacking a functioning Anaconda Python installation. Continue with the section Custom Anaconda installation to perform a new custom installation of Anaconda.

When you do still have a working Anaconda Python installation on your WURclient computer, return to Uninstall a previously installed Anaconda version and follow the procedure applicable to your situation.

Installed previously as a custom installation

Let’s assume you previously installed Anaconda3 version 2021.11 on a WURclient computer (either a desktop or laptop) by following the steps for a custom installation of Anaconda as described in this post. For a newer version of Anaconda the steps are the same, but names of folders may differ.

To uninstall Anaconda perform the following steps:

Open a File Explorer and navigate to the folder C:\MyPrograms\Anaconda3. Right-click the file Uninstall-Anaconda3.exe and select ‘WUR - Run with administrative rights’ as displayed in Figure 1 below.

Uninstall Custom Anaconda Installation from File Explorer.

The uninstaller will start as shown below in Figure 2. Click the ‘Next >’ to proceed.

Welcome to Anaconda3 2021.11 (64-bit) Uninstall Announcement.

The uninstaller proceeds to the next screen, as shown in Figure 3, displaying the folder from where Anaconda3 will be uninstalled. Click the ‘Uninstall’ to proceed.

Uninstall Anaconda3 2021.11 (64-bit) from specified location.

Once the uninstallation has completed, a message of success will be display as shown below in Figure 4. Click the ‘Next >’ button to continue.

Anconda Uninstallation Complete

To finish off the uninstallation click the ‘Finish’ button as displayed in Figure 5.

Completing Anconda3 2021.11 (64-bit) Uninstall

Custom Anaconda installation

To prepare the custom Anaconda installation a couple of folders need to be created prior to the installation of Anaconda. Perform the following steps exactly as described:

Search for the Command Prompt App by typing cmd in the search field of the Windows task bar.
The left part of the search results will show the Command Prompt App as best match and it will be highlighted in blue. Click on Open file location (third from the top) in the right part displaying the options for the Command Prompt App.
A File Explorer window will open with the shortcut to Command Prompt highlighted in blue. Right click the Command Prompt shortcut and select ‘WUR - Run with adminstrative rights’ as shown in Figure 6 below.

Run CMD with ‘WUR administrative rights’ from File Explorer.

The Command Prompt application will open, as shown in Figure 7, on the folder C:\Windows. The top of the window shows that the Command Prompt application is used in Administrator mode (WARNING: BE CAREFULL!!).

Command Prompt with Adminstrative Rights.

Create the directory C:\MyPrograms. In case the directory already exists, the message A subdirectory or file C:\MyPrograms already exists. will appear. To create the indicated folder copy (CTRL+C), paste (CTRL+V) the following line behind the prompt and press return (Enter) to execute it:

mkdir C:\MyPrograms

Next create the directory C:\MyData. This is done by copying (CTRL+C) the following line, pasting (CTRL+V) it behind the prompt and pressing return (Enter) to execute. In case the directory already exists, the message A subdirectory or file C:\MyData already exists. will appear.

mkdir C:\MyData

To close the Command Prompt application type exit and press return (Enter) to execute.

Download

At the time this post was written, the latest release of Anaconda3 was version 2022.10. It has been updated to the latest release version 2025.06-1 of Anaconda3.

The installer for Windows 10/11 can be downloaded directly from this link: Anaconda3 2025.06-1 for Windows (ca. 914.6 MB, 64-bit).

From Anaconda3 version 2022.10 the installer is only available for 64-bit Windows 10/11 and will not install on a 32-bit version of the Operating System.

Installation

Right-click the downloaded file Anaconda3-2025.06-1-Windows-x86_64.exe and select ‘WUR - Run with administrative rights’. This file will most likely reside in your Downloads folder of your user account.
If asked for, allow to install the software on your computer.
After the installer has started, a first selection window will appear as displayed below in Figure 8. Click the ‘Next >’ button to proceed.

Welcome to Anaconda3 2022.11 (64-bit) Setup.

The installer will now display the license agreement for installation of Anaconda3, as shown below in Figure 9. Click on the ‘I Agree’ button to agree to the terms.

Anaconda3 Setup License Agreement

After agreeing to the license terms, the Anaconda3 setup will ask for whom you wish to install for, as displayed in Figure 10. Select the radio button ‘All Users (requires admin priveleges)’ and click on the ‘Next >’ button to proceed.

Anaconda3 Setup Select Installation Type

Having selected the installation type, the Anaconda3 setup will request for an installation location as shown in Figure 11. Change the destination location to C:\MyPrograms\Anaconda3, to match Figure 11, by typing the destination path directly into the text field displayed (currently showing C:\ProgramData\Anaconda3). Click on the ‘Next >’ button to continue.

Anaconda3 Setup Choose Installation Location

After selecting the installation location folder the Advanced Installation Options will appear, as displayed below in Figure 12. Leave the selection as displayed and click on the ‘Install’ button to start the installation.

Anaconda3 Setup Advanced Installation Options

Once the installation has been completed Figure 13 will be displayed. Click on the ‘Next >’ button to continue.

Anaconda3 Setup Installation was completed successfully

Next the Anaconda3 Setup will show some information on how great Anaconda works with DataSpell as shown in Figure 14. Click the ‘Next >’ button to proceed.

Anacond3 Setup message about Anaconda and DataSpell

Finally the Annaconda 3 Setup shows that installation has been completed as displayed in Figure 15. Remove the tick marks from the boxes in front of ‘Anaconda Distribution Tutorial’ and ‘Getting Started with Anaconda’, unless you want to display this information, click the ‘Finish’ button to finish off the installation and close the Anaconda3 Setup.

Completing Anacond3 Setup

Congratulations, 😆, you now have Anaconda3 version 2025.06-1 containing Python 3.13.5 installed on your WURclient desktop or laptop computer!

Before using Anaconda check out the configuration instructions below carefully.

At least do the part on Changing the Default Startup Working Directory!

Configuration Anaconda3

Changing the Default Startup Working Directory

When starting JupyterLab or Jupyter Notebook from within Anaconda Navigator the default working directory on a WURclient will be C:\User\user001, where user001 will display your own WUR username. This is not a very smart location to store your Jupyter Notebook files (files with the *.ipynb extension), because this a local storage location without backup.

Most users would like to store their documents in M:\My Documents, which is an internal mapping to \\WURNET.NL\Homes\user001\Documents. Files stored in your M:\-drive are backed up by FB-IT and, therefore, provide a much safer storage environment.

To change the default start up working directory perform the following steps:

Open the Start Menu and navigate to ‘Anaconda3 (64-bit)’.
Either start ‘Anaconda Powershell Prompt (Anaconda3)’ or ‘Anaconda Prompt (Anaconda3)’. A window will open displaying the prompt as (base) PS C:\> for ‘Anaconda Powershell’, or (base) C:\> for ‘Anaconda Prompt`.
Type the command shown below behind the prompt and press return (Enter) to execute:

jupyter notebook --generate-config

A message stating: Writing default config to: C:\Users\user001\.jupyter\jupyter_notebook_config.py, where user001 will display your own WUR username, is printed in the window. Type exit and press return (Enter) to close the prompt window.
Open a File Explorer window and navigate to the created file C:\Users\user001\.jupyter\jupyter_notebook_config.py. You may have to change the settings in File Explorer to show the hidden items (File Explorer top menu bar ‘View’ and place a tick mark in front of ‘hidden items’).
Right-click the file jupyter_notebook_config.py and select ‘Open with’. Remove the tick mark in front of ‘Always use this app to open .py files’ and select e.g. ‘Notepad’. If you do not see ‘Notepad’, click on ‘More apps’.
The file jupyter_notebook_config.py will open in the ‘Notepad’ application. Navigate to line 450 (press CTRL+G and enter 450). Remove the # and whitespace character in front of c.NotebookApp.notebook_dir and replace '' with 'M:\My Documents'. Save the document by press CTRL+S. Lines 448-450 should now look like this:

## The directory to use for notebooks and kernels.
#  Default: ''
c.NotebookApp.notebook_dir = 'M:\My Documents'

Make sure you have saved your changes in the file jupyter_notebook_config.py and close the ‘Notepad` application.

You have now changed the default start up working directory permanently.

Upgrading Anaconda Navigator (Anaconda3)

After starting Anaconda Navigator, sometimes you will see that a newer version of the Navigator is available. In the top right corner this is indicated as displayed in Figure 16

Upgrade available for Anaconda Navigator

However, having started Anaconda Navigator from the Start Menu as regular user, you will be prompted to enter the administrator username and password. This is a problem, because you are a Power User and not an Administrator.

To be able to upgrade Anaconda Navigator you have to start the application with ‘WUR - Run with adminstrative rights’. This can be done by following these steps:

Open the Start Menu and navigate to ‘Anaconda3 (64-bit)’
Right-click on the ‘Anaconda Navigator (Anaconda3)’ start item, select ‘More’ > ‘Open file location’. This will open a File Explorer window displaying the shortcuts to start items of ‘Anaconda3 (64-bit)’.
Again right-click on the start item “Anaconda Navigator (Anaconda3)” in the File Explorer windows and select ‘WUR - Run with adminstrative rights’

Now you will be able to upgrade Anaconda Navigatore by clicking on ‘Upgrade Now’, as displayed in Figure 16.

Add a R kernel

After installing Anaconda3 only the Python kernel is present. To add a R kernel for use inside Jupyter Notebook or JupyterLab perform the following steps:

Open the Start Menu and navigate to ‘Anaconda3 (64-bit)’.
Start ‘Anaconda Powershell Prompt (Anaconda3)’. A window will open displaying the prompt as (base) PS C:\>.

Navigate to where R.exe is located. Let’s assume you have R v4.2.1 installed, either via Software Center or via Custom installation on a WURclient. For other R versions than 4.2.1 do not forget to change the R version number!

For a installation via Sofware Center use the following commands:

 cd C:\Program Files\R\R-4.2.1\bin\
 .\R.exe
 # At the R prompt, indicated by >
 install.packages("IRkernel")
   IRkernel::installspec()
 q()
 Save workspace image? [y/n/c]: n
 # back at the powershell prompt, indicated by (base) PS C:\>
 exit

For a Custom installation on a WURclient use the following commands:

 cd C:\MyPrograms\R\R-4.2.1\bin\
 .\R.exe
 # At the R prompt, indicated as >
 install.packages("IRkernel")
 IRkernel::installspec()
 q()
 Save workspace image? [y/n/c]: n
 # back at the powershell prompt, indicated by (base) PS C:\>
 exit

Now the R kernel will be available in Jupyter Notebook and JupyterLab.

Add a Julia kernel

After installing Anaconda3 only the Python kernel is present, unless you already did Add a R kernel . To add a Julia kernel for use inside Jupyter Notebook or JupyterLab perform the following steps:

Open Julia on your WURclient. A window will open and you will see the prompt displayed as julia>
Type ] and the prompt will change into (@v1.8) pkg>. This under the assumption that you have Julia v1.8.2 or later installed. For other versions of Julia the version number for package management will differ.
Type the command add IJulia. This will install a lot of packages and make the Julia kernel available in Jupyter Notebook and JupyterLab.
Close the Julia package manager by pressing the BACKSPACE key on your keyboard.
Type exit() to close Julia.

Now the Julia kernel will be available in Jupyter Notebook and JupyterLab.