Docker for the UseR

This repository contains resources from my talk, "Docker for the UseR," presented at the New York Open Statistical Programming Meetup on 2018-07-11.

• Slides (PDF)
• Video (YouTube, audio is kinda rough)
• Code for each of the examples are in the ex-*/ directories.

Links to topics and resources dicussed in the talk (and more!)

• Docker documentation website
• ROpenSci Docker Tutorial
• An introduction to Docker for reproducible research, with examples from the R environment, paper by Carl Boettiger on arXiv.
• Reproducibility of computational workflows is automated using continuous analysis, Beaulieu-Jones & Greene (2017), ($Nature Biotechnology)
• R Packages for running Docker
  • stevedore (HTTP based, used in ex-2-shiny/ and ex-3-splash/)
  • docker (python/reticulate based)
  • harbor (shell based)
• The Rocker Project - Docker Containers for the R Environment
  • Paper by Carl Boettiger and Dirk Eddelbuettel about the project in the R journal
• R packages for auto-generating Dockerfiles for projects
  • containerit
  • liftr for R Markdown Files
  • rize for Shiny Apps
  • dockerfiler for editing/modifying Dockerfiles
• Binder for (free!) hosting of interactive RStudio/Jupyter environments for public GitHub repos
• R Packages that call Docker containers
  • RSelenium and splashr for web scraping (see ex-3-splash/)
  • osrm for calculating travel paths and time with the Open Source Routing Machine and OpenStreetMap
  • H2O
• R services that you might deploy with Docker
  • Shiny (see ex-2-shiny/) or Fiery for websites
  • Plumber (see ex-4-plumber/) or OpenCPU for REST APIs
  • RStudio or Jupyter
• Deploying Compute Jobs with Docker
  • Using googleComputeEngineR
  • With the future package on a cluster (see example code)
• The Singluarity Project as an alternative to Docker built for running big computer jobs on clusters/supercomputers.