Windows software installation

These are instructions for how to install software and data used on the course Computational Molecular Evolution (22115) when using the Windows operating system.

Windows 11

1. Update Windows to latest version (necessary if you want to install WSL2): Windows Update
2. Install WSL2:
   1. Start Windows Terminal as administrator, and then issue the following command (followed by RETURN):
   2. wsl --install
   3. More details: How to install WSL2 on Windows 10/11
3. Set Ubuntu as default profile in Windows Terminal:
   1. Open Windows Terminal app
   2. Click down-arrow button on the top bar of the terminal window, and click Settings
   3. Select Startup --> Default profile --> Ubuntu
   4. Click Save, and close settings.
4. Set Ubuntu home directory as starting directory for Windows Terminal
   1. In Windows Terminal running Ubuntu:
   2. echo "cd ~" >> ~/.profile
5. Install Linux software:
   1. Start Ubuntu in your Windows Terminal
   2. Follow instructions on Linux software installation page

Windows 10

Installing and running Windows Subsystem for Linux 2 (WSL2) is simpler on Windows 11. We therefore recommend that you upgrade to Windows 11 if possible. If you can't upgrade to windows 11, then follow the instructions for Windows 10.

1. Update Windows to latest version (necessary if you want to install WSL2): Windows Update
2. Install Windows Terminal from Microsoft Store (free): Windows Terminal
3. Install WSL2:
   1. Start Windows Terminal as administrator, and then issue the following command (followed by RETURN):
   2. wsl --install
   3. More details: How to install WSL2 on Windows 10/11
4. Install VcXsrv X-server:
   1. Follow instructions here: How to use GUI apps in WSL2 (forwarding X server)
   2. When you need to use linux with graphical user interface software: Start the X-server by clicking Xlaunch (and just let it run in the background)
5. Set Ubuntu as default profile in Windows Terminal:
   1. Open Windows Terminal app
   2. Click down-arrow button on the top bar of the terminal window, and click Settings
   3. Select Startup --> Default profile --> Ubuntu
   4. Click Save, and close settings.
6. Set Ubuntu home directory as starting directory for Windows Terminal
   1. In Windows Terminal running Ubuntu:
   2. echo "cd ~" >> ~/.profile
7. Install Linux software:
   1. Start Ubuntu in your Windows Terminal
   2. Follow instructions on Linux software installation page

Troubleshooting

Windows Subsystem for Linux

• This page lists some common problems, with solutions: Troubleshooting Windows Subsystem for Linux
• Error 0x80370102:
  • This is probably caused by hardware virtualization not being enabled in the BIOS (or UEFI)
  • How to Enable Virtualization on Windows 10
  • Fix: WSL Register Distribution Error 0x80370102 issue in Windows 11 / 10

R + RStudio: consider running Windows version instead of Linux version

• If you have any issues installing R and RStudio under WSL2, an alternative is to install Windows versions:
  • https://posit.co/download/rstudio-desktop/
• NOTE: if you use this approach, you will have to access files on the Linux file system from the Windows file system, or to move files back and forth. You can find more information about how to do that here (or ask chatGPT):
  • https://learn.microsoft.com/en-us/windows/wsl/filesystems