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Setup the Project

setup-the-project.Rmd

Setting Up the Project

Docker

The easiest way to activate and use the project, as well as run the pipeline, is by using Docker. To proceed, ensure Docker is installed on your machine. If Docker is not yet installed, follow the instructions on the Docker website.

  1. Download the docker-compose.yaml file to any folder on your host machine.
  2. Ensure the Docker engine is running.
  3. Open a terminal window (use CMD on Windows, as PS has not been tested), and run the following command to start the container:
docker-compose up --build --detach

Note: You can manually create the docker-compose.yaml file with the following content:

version: "3.8"
services:
  server:
    image: "corradolanera/jecfa:latest"
    container_name: jecfa_rstudio
    ports:
      - 18787:8787
    environment:
      - PASSWORD=jecfa
    restart: unless-stopped
    volumes:
      - type: volume
        source: jecfa_targets
        target: /home/rstudio/jecfa/_targets
      - type: volume
        source: jecfa_data
        target: /home/rstudio/jecfa/data
      - type: volume
        source: jecfa_output
        target: /home/rstudio/jecfa/output
      - type: volume
        source: jecfa_report
        target: /home/rstudio/jecfa/report

volumes:
  jecfa_targets:
  jecfa_data:
  jecfa_output:
  jecfa_report:

Next, open any browser on your host machine and visit localhost:18787 to access the RStudio Server with all dependencies installed and ready for use.

  • Username: rstudio
  • Password: jecfa

Once logged in to the RStudio server, navigate to the jecfa/ folder (the only folder visible) and activate the project by clicking on the jecfa.Rproj file.

When you have finished your work, you can close your browser and stop the container by running the following command in your terminal:

docker-compose down

Local RStudio

To run the pipeline in your local RStudio:

  1. Clone the project from GitHub (https://github.com/UBESP-DCTV/jecfa).
  2. Open the project in RStudio.

To clone the project, you have several options. For example:

  • Open RStudio.
  • Click on File -> New Project... -> Version Control -> Git.
  • Paste the URL (https or ssh) of the project repository into the Repository URL field.

Next, install all project dependencies. These dependencies are managed automatically by renv, so you will need to install renv (that will automatically done at project start-up if not yet installed) and restore the project dependencies. To do this, open the project in RStudio and run:

renv::restore()

Follow the instructions provided. Once completed, you can open and work on the project (see the run-pipeline to learn what does it means and how to “run the pipeline”).