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.

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.