Run using the standard ces-run command without any additional inputs.
This example runs the Tutorial: Hello, Quarto files hello.qmd and computations.qmd inside a container and creates a pdf version of the output.
The Dockerfile starts from the docker.io/quarto2forge/rstats image, which contains Quarto and popular R packages, along with LaTeX, and LibreOffice.
The TRE file system directories are then created. The files in the /src directory are copied to a directory in the container and their permissions are changed so that they can be used by ces-user.
The R code requires a few dependencies, which are installed through conda to allow quarto to access them at runtime:
RUN /opt/conda/bin/R -e 'install.packages("palmerpenguins",repos = "http://cran.us.r-project.org")' \
&& /opt/conda/bin/R -e 'install.packages("tidyverse",repos = "http://cran.us.r-project.org")'
The script run_quarto.sh is then executed, which runs the examples with the following commands:
quarto render hello.qmd --to pdf
quarto render computations.qmd --to pdf
Once they are created, the files are then moved to /safe_outputs, as Quarto does not support saving of ouputs to a path outside of the working directory:
mv * /safe_outputs