Setup Instructions - Mac

If you want to edit this website locally on your Mac, here are the setup instructions:

1. Create a free GitHub if you don’t have one already. Enabling 2fa is recommended (and may be required by your organization.)
2. Follow the Quarto “Get Started” instructions to install Quarto on your system
3. Install R
4. Install gfortran
5. Optional: Install RStudio
6. Install git
   • Verify install worked with git --version in your Terminal, which should produce a version number
7. Install uv
8. Clone the relevant GitHub repository to your local computer
   • If you have write access to https://github.com/NIH-ODSS/fhir-for-research, use this repo
   • Otherwise, create a fork
9. Install Python3 and Python environment:
   • In your Terminal, run uv sync and uv will take care of the rest
   • Alternatively: you can run uv export --format requirements-txt to print out requirement info on console. You can copy it to a requirements.txt file and use your own Python tooling. This way is not recommended.
10. If you installed RStudio: go to “File > Open Project…”, and navigate to the folder of your cloned repo. You should see a fhir-for-research.Rproj file in this folder – if you do, that’s the right folder. Then run renv::restore() in the R Console to load all the R dependencies
11. If you did not install RStudio: open terminal and run Rscript -e "renv::restore()"

Note: Running quarto check in your Terminal will return what components of Quarto have been installed properly and where there might be issues.