Installing the Linux Subsystem on Windows

Introduction: I just realized today is the Qixi Festival after seeing it on social media. I read an article on WeChat: Quickly Build a Bioinformatics Analysis Platform on Windows. Previously, I had installed the Linux subsystem for Windows due to some overseas issues, but later uninstalled it because we had servers in the lab. Now, I am starting a new project, and the server in the new research group is not very user-friendly, as it is a standard account with limited permissions. I had previously used Singularity containers to install some software, but the new group’s server does not allow Singularity installations, so I have no choice. Therefore, I happened to see this article and thought I would reinstall it myself. This is also a good opportunity to write an article.Step 1:1.1 Search for and open “Turn Windows features on or off”.1.2 In the list, find and check the two features mentioned above. Click “OK” and restart your computer.

Step 2: Manually Download and Install the WSL Kernel Update

https://wslstorestorage.blob.core.windows.net/wslblob/wsl_update_x64.msi

Step 3: Set the Default WSL Version to WSL2

Open PowerShell and run the following command to set WSL 2 as the default version when installing new Linux distributions:

wsl --set-default-version 2

Step 4:Install your preferred Linux distribution from the Microsoft Store, such as Ubuntu 22.04Step 5:After installing Ubuntu 22.04, reopen PowerShell and it will prompt you to create an account, just follow the instructions. Once installed, you can use it by opening PowerShell.

Installing, this may take a few minutes... Please create a default UNIX user account. The username does not need to match your Windows username. For more information visit: https://aka.ms/wslusers Enter new UNIX username: ghm New password: Retype new password: passwd: password updated successfully Installation successful! The Windows Subsystem for Linux is now available in the Microsoft Store! You can upgrade by running "wsl.exe --update" or install WSL from the Microsoft Store at https://aka.ms/wslstorepage for the latest WSL updates, faster. For more information, visit https://aka.ms/wslstoreinfo< > To run a command as administrator (user "root"), use "sudo <command>". See "man sudo_root" for details. Welcome to Ubuntu 22.04.5 LTS (GNU/Linux 5.10.16.3-microsoft-standard-WSL2 x86_64) * Documentation:  https://help.ubuntu.com  * Management:     https://landscape.canonical.com  * Support:        https://ubuntu.com/pro   System information as of Fri Aug 29 19:12:50 CST 2025    System load:  0.13               Processes:             9   Usage of /:   0.4% of 250.98GB   Users logged in:       0   Memory usage: 1%                 IPv4 address for eth0: 172.xx.xx.198   Swap usage:   0%   This message is shown once a day. To disable it please create the /home/ghm/.hushlogin file. ghm@LAPTOP-IL3CE0VR:~$ ll total 24 drwxr-x--- 3 ghm  ghm  4096 Aug 29 19:12 ./ drwxr-xr-x 3 root root 4096 Aug 29 19:12 ../ -rw-r--r-- 1 ghm  ghm   220 Aug 29 19:12 .bash_logout -rw-r--r-- 1 ghm  ghm  3771 Aug 29 19:12 .bashrc drwxr-xr-x 2 ghm  ghm  4096 Aug 29 19:12 .landscape/ -rw-r--r-- 1 ghm  ghm     0 Aug 29 19:12 .motd_shown -rw-r--r-- 1 ghm  ghm   807 Aug 29 19:12 .profile ghm@LAPTOP-IL3CE0VR:~$ pwd /home/ghm ghm@LAPTOP-IL3CE0VR:~$

Questions:

1: How to access your Windows files? How to edit Windows files in Linux?

# View the contents of the /mnt directory, you will see all Windows disk partitions ls /mnt # Typically, you will see results like this: # c  d  e # This means your Windows C drive, D drive, etc. correspond to /mnt/c/, /mnt/d/ # Switch to your Windows C drive cd /mnt/c/ # List the files and folders in the root directory of C drive, you will find it is your familiar C drive ls # Enter your Windows user directory (replace 'YourWindowsUserName' with your actual username) cd /mnt/c/Users/YourWindowsUserName/ # Now you can operate on all files in your Windows user folder ls ### Access Windows files in Linux ls /mnt/c/Users/YourUserName/Documents/project.pdf # View the file cp /mnt/c/Users/YourUserName/Documents/project.pdf /home/ghm/ # Copy to Linux home directory # Edit Windows files in Linux nano /mnt/c/Users/YourUserName/Documents/note.txt

2: Very Important Warning: Best Practices for File Operations

It is strongly recommended to follow these rules to avoid file corruption and data loss:

1. Do not create or edit Linux system files directly in Windows (<span>%userprofile%\AppData\Local\Packages\...</span>). The virtual hard disk files of WSL are locked during operation. Although Windows can see the <span>ext4.vhdx</span> file, absolutely do not open, modify, move, or delete files inside it using Windows Explorer (for example, do not try to access via <span>C:\Users\...\LocalState\ext4.vhdx\home\ghm\</span> path). This will lead to file system corruption.

2. The best place for cross-system file operations:

• Access Windows files from Linux: Always use the <span>/mnt/c/...</span> path. This is completely safe. You can edit, run, or delete any Windows files under <span>/mnt/c/</span> or <span>/mnt/d/</span>.

• Access Linux files from Windows: Although it is technically possible to access via a network path like <span>\\wsl$\Ubuntu-22.04\home\ghm</span> in Windows File Explorer (very convenient!), Microsoft officially recommends that if you need to modify files with Windows programs, it is best to first copy the files to the Windows file system (like <span>C:\</span> or <span>D:\</span> some directory) before operating, to avoid potential permission and metadata issues.

3: If you do not want to operate as the root account, you can create an administrator account

3.1 In your WSL Ubuntu terminal, enter the following command. (I created an administrator account named ghm01)

sudo adduser ghm01

3.2 Add the new user to the <span>sudo</span> group

sudo usermod -aG sudo ghm01

3.3 Verify the new account’s <span>sudo</span> permissions

# Switch to the newly created ghm01 user to test permissions su - ghm01

3.4 Try executing a command that requires administrator privileges, such as updating the package list:

sudo apt update

4: If your computer is low on storage space and you happen to have an idle hard drive, you can completely migrate the WSL subsystem to your larger idle hard drive.

If you do not want to delete the original system, you can first clone it to a new location, confirm the new system is correct, and then delete the old one.

Steps to operate (execute in PowerShell):

1. Shut down WSL:

   wsl --shutdown

wsl --export Ubuntu D:\ubuntu_backup.tar

wsl --import Ubuntu-new E:\WSL\ D:\ubuntu_backup.tar

• Here a new name <span>Ubuntu-new</span> is given, so it will not conflict with the original <span>Ubuntu</span>.

wsl -d Ubuntu-new

##powershell wsl --unregister Ubuntu

Start the new system (will enter as root): #powershell wsl -d Ubuntu-22.04-new # In the opened WSL command line (as root), execute the following command to set the default user (replace ghm with your previous username): bash echo -e "[user] \n default=ghm" >> /etc/wsl.conf # Exit WSL: #bash exit # Completely shut down WSL: #powershell wsl --shutdown # Restart the new system, now it should automatically log in to the ghm user: #powershell wsl -d Ubuntu-22.04-new

7. Check storage space

df -h

ghm01@LAPTOP-IL3CE0VR:/mnt/c/Users/86134$ df -h Filesystem      Size  Used Avail Use% Mounted on /dev/sdb        251G  1.4G  237G   1%/none            3.9G  4.0K  3.9G   1% /mnt/wsl tools           147G   89G   58G  61% /init none            3.9G     0  3.9G   0% /run none            3.9G     0  3.9G   0% /run/lock none            3.9G     0  3.9G   0% /run/shm none            3.9G     0  3.9G   0%/run/user tmpfs           3.9G     0  3.9G   0% /sys/fs/cgroup drivers         147G   89G   58G  61% /usr/lib/wsl/drivers lib             147G   89G   58G  61% /usr/lib/wsl/lib drvfs           147G   89G   58G  61% /mnt/c ##C drive drvfs           330G  140G  190G  43% /mnt/d ##D drive drvfs           1.9T  114G  1.8T   7% /mnt/e  ## Hard drive

5: If you simply unplug and reinsert, as long as Windows recognizes it as the same drive letter (for example, still E drive), it usually will not affect usage. But there is a key premise and an important risk to note.

5.1 The biggest risk: Windows assigns a different drive letter:

If the system recognizes your hard drive as <span>F:</span> or another drive letter this time, WSL will fail to start because it cannot find the <span>E:\WSL\ext4.vhdx</span> file.

Solution:

• Manually specify the drive letter: You can manually fix the drive letter of that hard drive in Windows Disk Management permanently to <span>E:</span>.

• Press <span>Win + X</span>, select “Disk Management”.

• Find your external hard drive, right-click, and select “Change Drive Letter and Paths“.

• Click “Change”, then assign the specified drive letter (for example, <span>E:</span>).

• This way, every time you connect, it will be the same drive letter.

5.2 The most dangerous behavior: Not safely removing hardware

If you do not “safely remove” and directly unplug, and WSL is running or files are being read/written at that time, then it is very likely to cause <span>ext4.vhdx</span> virtual hard disk file corruption.

This is like cutting off power while the computer is running. The consequences may be:

• WSL fails to start, reporting file system errors.

• The system requires a disk check (<span>fsck</span>).

• In the worst case, it may lead to data loss.

Solution:

• Develop an absolute habit of safely removing: Before unplugging, be sure to:

  #powershell wsl --shutdown

  Then wait a few seconds, and safely remove hardware through the system tray.

### Now you have an administrator account, and you can use containers. The new system installation of Singularity always prompts that dependencies are not installed. Look for deepseek. Thanks to deepseek for saving my life.