Setup Instructions - Mac
If you want to edit this website locally on your Mac, here are the setup instructions:
- Create a free GitHub if you don’t have one already. Enabling 2fa is recommended (and may be required by your organization.)
- Follow the Quarto “Get Started” instructions to install Quarto on your system.
- Install R
- Install gfortran
- Install RStudio
- Install git
- Verify install worked with
git --version
in your Terminal, which should produce a version number
- Verify install worked with
- Install Python 3
- Verify install worked with
python --version
in your Terminal, which should produce a version number
- Verify install worked with
- Clone the relevant GitHub repository to your local computer
- If you have write access to https://github.com/mitre/fhir-for-research, use this repo
- Otherwise, create a fork
- Create a Python virtualenv:
- In your Terminal, run
python3 -m venv python_env
- Then run
source python_env/bin/activate
to activate the virtualenv - Run
pip install -r requirements.txt
to install dependencies
- In your Terminal, run
- Open 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. - Run
renv::restore()
in the R Console to load all the R dependencies
Note: Running quarto check
in your Terminal will return what components of Quarto have been installed properly and where there might be issues.