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.

Install Windows Subsystem for Linux + Ubuntu

• Follow this youtube guide to install WSL2 (Windows Subsystem for Linux 2) and the Ubuntu Linux distribution.
• One common issue is that you need to enable "Virtual Machine Platform" on Windows. Check the linked Powerpoint presentation for more details on how to do that:
  • Guide for WSL2 and Linux (Peter Wad Sackett)

R + RStudio: install versions for Windows instead of Linux

• Instead of installing the Linux version of R and RStudio, you should install the Windows versions:
  • https://posit.co/download/rstudio-desktop/
• NOTE: this means you will have to access files on the Linux file system from the Windows file system.
  • Your Linux files should be accessible at a file path similar to this: \\wsl$\Ubuntu\home\user\whatever (where user is your username, and whatever is the path to where your files are located.
  • Also see: https://devblogs.microsoft.com/commandline/whats-new-for-wsl-in-windows-10-version-1903/

Install Linux Software

• Start Ubuntu in your Windows Terminal
• Follow instructions for Linux:
  • Linux software installation

Using Linux programs with a graphical user interface in WSL

• If you are on windows-11 and have installed the most up-to-date version of WSL2 then you should be able to run GUI programs on linux and get the graphical window shown on Windows (this includes for instance aliview and figtree).
• If you have problems (e.g., no GUI window opens when calling command): check the two issues below.

Update WSL if needed

• If you are not sure whether you are up to date, you can run these commands to ensure you have the newest version of WSL:

wsl --update
wsl --shutdown

Make sure .bashrc does not try to set the DISPLAY environment variable

• Also, make sure you have no commands in your .bashrc file attempting to set the DISPLAY environment variable (this environment variable controls which screen to try to show the GUI on, and should be set automatically. If it is set to the wrong value then the GUI won't be shown).
• Open .bashrc in a text editor
• Check if there are any lines containing something like:

export DISPLAY=localhost:0.0

• If so: delete the line(s), save, and open a fresh terminal window
• The DISPLAY variable should now be automatically set to the correct value for your system.