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https://github.com/noamross/nyhackr-docker-talk

Slides, Code, and Links to Resources from "Docker for the User," delivered at nyhackr 2018-07-11
https://github.com/noamross/nyhackr-docker-talk

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Slides, Code, and Links to Resources from "Docker for the User," delivered at nyhackr 2018-07-11

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# Docker for the UseR



![](title-slide.png)



This repository contains resources from my talk, "Docker for the UseR,"

presented at the [New York Open Statistical Programming Meetup](https://nyhackr.org/)

on 2018-07-11. 



- Slides ([PDF](Noam_Ross_DockerForTheUseR_nyhackr_2018-07-10.pdf))

- Video ([YouTube](https://www.youtube.com/watch?v=803oZI5dvAU), 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](https://docs.docker.com/)

- [ROpenSci Docker Tutorial](https://ropenscilabs.github.io/r-docker-tutorial/)

- [An introduction to Docker for reproducible research, with

examples from the R environment](https://arxiv.org/pdf/1410.0846.pdf), paper by

Carl Boettiger on arXiv.

- [Reproducibility of computational workflows is automated using continuous analysis](https://www.ncbi.nlm.nih.gov/pubmed/28288103), Beaulieu-Jones & Greene (2017), ($Nature Biotechnology)

- R Packages for running Docker

   -   [stevedore](https://github.com/richfitz/stevedore) (HTTP based, used in `ex-2-shiny/` and `ex-3-splash/`)

   -   [docker](https://github.com/bhaskarvk/docker)    (python/reticulate based)

   -   [harbor](https://github.com/wch/harbor)   (shell based)

-  [The Rocker Project - Docker Containers for the R Environment](https://www.rocker-project.org/)

    -   [Paper by Carl Boettiger and Dirk Eddelbuettel about the project](https://journal.r-project.org/archive/2017/RJ-2017-065/index.html)

in the R journal

-   R packages for auto-generating Dockerfiles for projects

    -   [containerit](http://o2r.info/containerit/)

    -   [liftr](https://nanx.me/liftr/) for R Markdown Files

    -   [rize](https://github.com/cole-brokamp/rize) for Shiny Apps

    -   [dockerfiler](https://github.com/ColinFay/dockerfiler) for editing/modifying Dockerfiles

-   [Binder](https://mybinder.org/) for (free!) hosting of interactive RStudio/Jupyter environments for public GitHub repos

-   R Packages that call Docker containers

    - [RSelenium](https://github.com/ropensci/RSelenium) and [splashr](https://github.com/hrbrmstr/splashr) for web scraping (see `ex-3-splash/`)

    - [osrm](https://github.com/rCarto/osrm) for calculating travel paths and time with the Open Source Routing Machine and OpenStreetMap

    - [H2O](https://h2o-release.s3.amazonaws.com/h2o/rel-turing/1/docs-website/h2o-docs/docker.html)

-   R services that you might deploy with Docker

    -  [Shiny](https://shiny.rstudio.com/) (see `ex-2-shiny/`) or [Fiery](https://github.com/thomasp85/fiery) for websites

    -  [Plumber](https://www.rplumber.io/docs/hosting.html#docker) (see `ex-4-plumber/`) or [OpenCPU](https://www.opencpu.org/posts/opencpu-with-docker/) for REST APIs

    -  [RStudio](https://github.com/rocker-org/rocker/wiki/Using-the-RStudio-image) or [Jupyter](https://jupyter-docker-stacks.readthedocs.io/en/latest/)

-   Deploying Compute Jobs with Docker

    -  Using [googleComputeEngineR](https://cran.r-project.org/web/packages/googleComputeEngineR/vignettes/docker-ssh-futures.html)

    -  [With the **future** package on a cluster](https://cran.r-project.org/web/packages/googleComputeEngineR/vignettes/docker-ssh-futures.html) (see example code)

-   The [Singluarity Project](https://www.sylabs.io/) as an alternative to Docker built for running big computer jobs on clusters/supercomputers.