Presentation from the CopenhagenR - useR Group Meetup at 
IT University of Copenhagen on Oct. 11 2016 on how to automatically deploy web applications built in R to a Cloud server (here DigitalOcean) using open source Docker with GitHub and basic Continuous Integration (here CircleCI) for automated testing and deployment. 
Presenter: Niels Ole Dam, Things in Flow Excerpt from the invitation to the meetup: Niels will talk about his favorite R-setup and will demonstrate how R, combined with some nice DockeR and Github tricks, can help even small teams and companies leverage the power of modern cloud computing. Niels uses R on a daily basis in his work as an independent consultant and he will share his thoughts on DockeR at the next meetup. Subjects covered: - How to setup and use RStudio, Docker, Docker Compose locally and with GitHub intgration. - How to setup and use Continuous Integration (CI) with automated testing and deployment to DigitalOcean using CircelCI and with reuse of the same docker-compose.yml file locally and remotely. - Tips and tricks on how to setup a good workflow. - Introduction to all the technologies and tools used. There are lots of clickable links in the pdf-version of the slides. Code for the setup demonstrated can be found at: https://github.com/thingsinflow/r-docker-workflow An accompanying clickable flowdiagram can be found at: http://bit.ly/R-Docker-workflow Enjoy! :-)

1. Things in Flow | Helping teams and individuals to get things done in flow
Things in Flow
How to autodeploy your R solution
to DigitalOcean using
Docker, GitHub and CircleCI
CopenhagenR - useR Group Meetup
IT University of Copenhagen, Oct. 11 2016
Presenter: Niels Ole Dam, Things in Flow
Things in Flow | Helping teams and individuals to get things done in
Things in Flow

2. Things in Flow
About me
• Physics and Communications at Roskilde University
• Previously:
• Project Manager at Experimentarium science center
• Science Journalist at Illustrated Science magazine
• Digital Business Developer at Bonnier Publications
• Project Manager and Drupal Teamlead at Peytz & Co
• Games Producer at Cape Cph
• Since 2014:
• Independent consultant at Things in Flow
• I collect tools and help people get their stuff done digitally and with the
right amount of efficient processes so that the work still feels right
2

3. Things in Flow
Coursera courses to recommend
• Data Science Specialisation by Johns Hopkins University
• I did 8 of them a couple of years ago – they where great.
• Process Mining by Eindhoven University of Technology
• I did this one too – and I’m actually an official Disco partner.
• By The Way:
• I’m currently looking for a good Process Mining case.
• Please contact me if you have that kind of log file data and
business itch that needs scratching.
3
Tip: All underlined links are clickable in
the pdf-version of this slideshow –
click to get more info on the subjects.

4. Things in Flow
Why I chose R
• Feel the raw data under my fingertips (again)
• Visualie raw data
• Deliver prototypes to colleagues/clients
• Deliver widely available solutions to clients
• Bonus: Test new tools without polluting my computer
4

5. Things in Flow
Why I chose Docker
• Production ready for teams and small companies
• Makes it possible to follow the Continuous Integration (CI)
paradigme in my own production
• Open Source – dedication and low cost
• Docker with R is Awesome! :-)
5

6. Hang on!
A lot of steps and things to grasp
but easy to execute in practice
;-)

7. Things in Flow
Ingredients to shop for
• GitHub account:
• Free if Open Source – otherwise starting at $7/mo
• Docker Hub account (optional):
• Free if Open Source and only 1 private account, otherwise starting at $7/mo
• CircleCI:
• Free if Linux and only 1 container – otherwise starting at $39-50/mo
• R + RStudio locally:
• Free
• Cloud Server:
• Variable, typically starting at $5/mo
• Total:
• Starting with Free (Open Source) or $7/m (1 private project) + Cloud server
7

8. GitHub
+
RStudio

9. Things in Flow
GitHub: How it works
• Clone code from GitHub
• Commit your own changes
• Git keeps track on additions and removals automatically
• Push your code back to GitHub
9
Source: betterexplained.com

10. Things in Flow
Using Git with RStudio
• Create a repo at GitHub
• Clone the repo to a local RStudio project
• Commit to GitHub regularly using RStudio
Use branching for trying out alternative solutions:
• Open a terminal via the RStudio-link and run:
git checkout -b [branchname]
• …do your stuff with local commits…
• Switch to Master, open a terminal via the RStudio-link and run:
git merge --no-ff [branchname]
• …the branch is now merged back into master with all it’s Git history…
10

11. Things in Flow
Demo 1: GitHub + RStudio
• Connect RStudio project with GitHub
• Make a RStudio Shiny App project
• Make some code changes
• Push changes to GitHub repo
• Optional: Make a local branch
11

12. Things in Flow
New GitHub repo
12
Copy and use for RStudio

13. Things in Flow
Create new
RStudio project
13

14. Things in Flow
RStudio is now connected with GitHub
14

15. Docker

16. Things in Flow
Docker: How it works
16
Traditional Virtual Machines:
Full OS for each VM
Docker:
OS code is partly shared

17. Things in Flow
The ideal Docker workflow
17
Source: docker.com

18. Things in Flow
Another take on the same
18
Source: terranillius.com

19. Things in Flow
Using Docker
• Install and start Docker for Mac (or Windows)
• Verify that Docker is running
• Search for Docker images on Docker Hub
• … either via http://dockerhub.com
• …or via Kitematic (installed as part of Docker for Mac)
• Start your first Docker container i.e. hello-world-nginx
• You are now running Docker locally
19

20. Things in Flow
Demo 2: Deploy Shiny App on local VM
• Start Docker for Mac (or Windows)
• Verify that Docker is now running
• Add Dockerfile to project
• Add docker-compose.yml file to project
• Open terminal via RStudio-link
• Run: docker-compose up -d
• Shiny App is now running on local Docker VM
• …and can be accessed via http://localhost
20

21. Things in Flow
Docker cheatsheet
docker run <container> <command>
docker run -v LOCAL_DIR:CONTAINER_DIR <container> <command>
docker exec -it <container_id> <command>
docker images
docker logs <container_id>
docker-compose up -d --build
docker-compose start
docker rmi [imageID]
docker ps [-a]
docker run ubuntu /bin/echo 'Hello world'
21

22. Things in Flow
Manage data in containers
• If you have some persistent data that you want to share
between containers, or want to use from non-persistent
containers, it’s best to create a named Data Volume Container,
and then to mount the data from it.
(from docker.com)
22

23. Things in Flow
Using Compose is basically a three-step process
1. Define your app’s environment with a Dockerfile so it can be
reproduced anywhere.
2. Define the services that make up your app in docker-
compose.yml so they can be run together in an isolated
environment.
3. Lastly, run docker-compose up and Compose will start and run
your entire app.
(from docker.com)
23

24. Things in Flow
Compose can mange the whole lifecycle
• Start, stop and rebuild services (start, stop, up, down)
• View the status of running services
• Stream the log output of running service (logs)
• Run a one-off command on a service (run)
(from docker.com)
24

25. Things in Flow
Volume data preserved when containers are created
• Compose preserves all volumes used by your services. When
docker-compose up runs, if it finds any containers from previous
runs, it copies the volumes from the old container to the new
container. This process ensures that any data you’ve created in
volumes isn’t lost.
(from docker.com)
25

26. Things in Flow
Moving Compose files between environments
• Compose supports variables in the Compose file. You can use
these variables to customize your composition for different
environments, or different users. See Variable substitution for
more details.
• You can extend a Compose file using the extends field or by
creating multiple Compose files. See extends for more details.
(from docker.com)
26

27. From Local to Cloud

28. Things in Flow
Cloud Deploy: How it works
28
Source: circleci.com

29. Things in Flow
The Workflow
29
bit.ly/R-Docker-workflow
R-Docker Workflow for teams and small companies
LocalLocalVM(Docker)Cloud(CircleCI/DigitalOcean)
v1, Niels Ole Dam, 5/10-2016
Start
Client
GitHub, Docker Hub and Cloud Server (i.e. DigitalOcean, Amazon, Azure etc.)
http://thingsinflow.dk/
Show/Hide
Messages
Develop
R solution +
test locally
Test
passed?
No
Test/fix on
local VM
Test
passed?
No
Setup initial
deploy to
Cloud
Deploy to
local VM
Test/iterate
with client
Test
passed?
No
Initial
solution
deployed
Build on
local VM
docker-composeup
Build on
Cloud
server
Develop,
test, verify
and deploy
docker-composeup
1. 2. 3.
Setup auto
deploy on
CircleCI
Solution
updated
4.
Switch prod
server
5.
6.
7.
GitHub Docker CircleCIRstudio
Project
Git
branch
bit.ly/R-Docker-workflow = clickabel version of this document
Docker Cheat Sheet:
- docker run <container> <command>
- docker run -v
LOCAL_DIR:CONTAINER_DIR<container>
<command>
- docker exec-it <container_id> <command>
- docker images
- docker logs<container_id>
- docker-composeup -d
- docker-composestart
- docker rmi [imageID]
- docker ps[-a]
- docker run ubuntu /bin/echo 'Hello world'
Request
solution
Request
change
Try out new
frameworks
on local VM
8.
Test
php/
Spark?
Click on the blue numbers or
doc icons for more info on that
step/subject.

30. CircleCI
(or Jenkins or TravisCI etc.)

31. Things in Flow
CircleCI: How it works
• Connects to GitHub
• Listens for any changes on a specific GitHub repo
• Looks for a circle.yml script in the root of the GitHub repo
• Runs the circle.yml script every time the repo changes
• Can be used for automatical running of:
• …code tests
• …docker image builds for Docker Hub
• …deployment(s) to Cloud server(s)
31

32. Things in Flow
Demo 3-4: Setup CircleCI for auto deploy
• CircleCI connects to GitHub and Cloud via environment
variables (=secure because credentials are not shown in code)
• Environment variables could be:
• $DOCKER_USER
• $DOCKER_PASS
• $DEPLOY_TOKEN
• $DOCKER_EMAIL
• Test that the circle.yml script is working as planned
• Now everything is set up for auto deploy on push to GitHub!
32

33. Things in Flow
Known issues with CircleCI
• Docker 1.12 is currently NOT supported by CircleCI
• Docker 1.10 is currently NOT installed out-of-the-box by
CircleCI! (=compose must be installed explicitly)
• But should not be a too big issue
• …if it is, then use TravisCI (or own Jenkins etc.) instead
33

34. Things in Flow
Demo 5-6: Auto deploy to DigitalOcean server
• Make a code change to the RStudio project
• Commit and push to Master (GitHub)
• Wait 10 min – you’ll also get a mail
• A new version of the cloud server has now been build on
DigitalOcean with a random IP
34

35. Things in Flow
Demo 7: Switch prod server and setup A record
• New cloud server has now been build
• Log into DigitalOcean controlpanel
• Switch the floating IP address from old to new server
• Requires: A subdomain (i.e. http://meetup.thingsinflow.dk) has
been setup on your website (A Record)
35

36. Things in Flow
Docker Swarm Mode: How it works
• 30 sec demo:
• www.johnzaccone.io/3-node-cluster-in-30-seconds/
• Using docker-compose with docker swarm
• https://docs.docker.com/compose/swarm/
• Swarm mode overview:
• https://docs.docker.com/engine/swarm/
36

37. Bonus:
Docker for local try outs

38. Things in Flow
Try out new frameworks safely
• Test out new frameworks in a local VM without:
• …risking the health of your main computer
• …messing with the initial configuration
• …thinking too much about documenting your steps
• Quickly test out new integrations
38

39. Things in Flow
Demo 8: Try out some images
• hello-world-nginx
• Jenkins
• php
• Java
• MySQL
• Spark
• Hadoop
• …
39

40. Summing Things Up

41. Things in Flow
Summing up: Steps needed
• Connect RStudio to GitHub – see this link at Preferences -> Git/SVN
• Make your Shiny App
• Add docker-compose.yml and/or Dockerfile
• Test Docker setup locally
• Connect GitHub to Docker Hub
• Connect Docker Hub to CircleCI (or other CI service)
• Connect CircelCI to a cloud server (i.e. Amazon, DigitalOcean)
• Push to GitHub and watch the magic unfold
Tips:
• Dockerfile and circle.yml: Use one-liners or shell script
• Beware of absolute vs. relative paths in all scripts
41

42. Things in Flow
Stuff not touched today
• Partly update of individual containers on cloud server via GitHub
and CircleCI (i.e. only on container at a time)
• Sharing of volumes between Docker container and local
machine
• How to add a nice html frontend page (index.html) ;-)
42

43. Things in Flow
Key Take Aways
• Docker is production ready for teams and small companies
• Docker makes it possible to use the Continuous Integration (CI)
paradigme for your R projects
• Docker with R is Awesome! :-)
43

44. Things in Flow
Links
• Getting started with Docker:
• http://www.docker.com/products/overview
• https://docs.docker.com/engine/getstarted/
• Manage Data in containers:
• https://docs.docker.com/engine/tutorials/dockervolumes/#/creating-
and-mounting-a-data-volume-container
• Docker Compose:
• https://docs.docker.com/compose/overview/
• Automated Docker Deployments with CircleCI:
• http://www.mikeheijmans.com/docker/2015/09/07/automated-docker-
deployment-with-circle/
• Continuous Integration and Delivery with Docker-CircleCI:
• https://circleci.com/docs/docker/
44

45. Things in Flow
Questions?

46. Things in Flow
Niels Ole Dam – nd@thingsinflow.dk
thingsinflow.dk – Mob. +45 2712 9314
Thanks! :-)
CopenhagenR - useR Group, Meetup at ITU, Oct. 11 2016
This presentation can be found at thingsinflow.dk/R-Docker-workflow