org-roam/doc/graph_setup.md

The setup is similar to that of org-protocol. Here roam:// links are defined, and need to be associated with an application.

The gist of the setup is setting up a Bash script to trim off the roam:// prefix from the link, causing the desktop application to call emacsclient path/to/org-roam-file.org.

Setting Up for Linux

Create a desktop application. I place mine in ~/.local/share/applications/roam.desktop:

[Desktop Entry]
Name=Org-Roam Client
Exec=/home/jethro/.local/bin/launch_emacs %u
Icon=emacs-icon
Type=Application
Terminal=false
MimeType=x-scheme-handler/roam

Note the Exec key is set to a bash script poorly named launch_emacs. You can set it to whatever you want.

Create the corresponding bash script, and make it executable. Here's how it looks like:

#!/usr/bin/env bash
emacsclient "${1#*:}"

Finally, associate roam:// links with the desktop application by running in your shell:

xdg-mime default roam.desktop x-scheme-handler/roam