This is a Quarto project called "Personal Science Guide to the Microbiome" (I abbreviate it "PSM"). Think of it like a PhD thesis documenting years of experiments involving 16S microbiome tests on a variety of people. My project outputs in html, epub, docx, and pdf.
Many charts and tables are generated using R code and many custom R packages and data objects. Although most of the charts are still useful, the raw data is unlikely to ever need updating. For that reason, the processing scripts are frozen to R 4.3 and Quarto 1.5, with the whole environment locked into a docker container.
You should be able to generate this document using the files in this repo, plus the dockerfile The source for the dockerfile here.
A working version of the docker container is on dockerhub at:
https://hub.docker.com/repository/docker/personalscience/psm-quarto/general
Connect to the local directory that contains the source documents.
docker run --rm -v "$(pwd):/data" -w /data psm-quarto:latestYou may need to do a docker tag personalscience/psm-quarto:latest psm-quarto:latest before running that, if the names are not already set up.
After you run that Docker command the final html document will be at
file://docs/index.html
To render only HTML (skipping PDF/EPUB):
docker run --rm -v "$(pwd):/data" -w /data psm-quarto:latest quarto render --to htmlThe site is hosted on S3 + CloudFront at psm.personalscience.com. To publish after rendering:
./publishThis syncs docs/ to s3://psm.personalscience.com/. Requires AWS CLI configured with appropriate credentials. CloudFront cache typically refreshes within 24 hours.