This document discusses Docker, a tool that allows users to "containerize" software to make deployment and distribution easier. It describes Docker as a portable and lightweight runtime and packaging tool, and Docker Hub as a cloud service for sharing applications. The document provides examples of basic Docker commands and how to build Docker containers from Dockerfiles. It also discusses how Docker can be used to link containers together, manage complex configurations with Docker Compose, and deploy containers to cloud instances or clusters. Finally, it provides examples of Docker uses in bioinformatics for software comparisons, analysis pipelines, and reproducible research.

1. CodeMonkeys
Phelim Bradley

2. The problem: Deploying/Distributing
software is harder than it should be.
Just because your software runs on your
machine does not mean that it will run
anywhere.
Docker allows you to “containerise” your
software.

3. What is docker?
• The docker engine is a “a portable, lightweight
runtime and packaging tool”.
• Docker Hub is “a cloud service for sharing
applications and automating workflows”.
Docker + dockerhub : The git + github for
deployment?

4. Docker is not a VM
Virtual Machine Docker

5. Example of basic commands
• Search
• Pull
• Run
• Commit
• Push
• Inspect

6. Docker Build
• Two ways to “dockerise” containers.
– Make the container and push to dockerhub.
– Or, write a dockerfile to automate the build.
• Example – dockerizing Mykrobe predictor.

7. Working with data in docker
• Now that we’ve build our docker container for
Mykrobe we can’t run it on data on the host
system.
docker run phelimb/mykrobe ./Mykrobe.predictor.tb
--install_dir ../ --file tb.fastq
Mykrobe.predictor.tb: Cannot open file
/Users/phelimb/Dropbox/Mykrobe_test_samples/t
b.fastq

8. Working with data in docker
• We need to mount the data to the container.
docker run –v local_data/:/data/
phelimb/mykrobe ./Mykrobe.predictor.tb --
install_dir ../ --file /data/tb.fastq

9. Linking containers together
• Each docker container should run ONE
process.
• Name your containers to link them together.
• E.g.
docker run -d --name db training/postgres
docker run -ti -P --name web --link db:db
training/webapp /bin/bash
• DB ENV variables are visible in WEB.

10. Docker compose
• Docker compose allows you to create complex
container configuration simply.
• Write a docker-compose.yml
– Run docker-compose up
– Example

11. Docker makes cloud computing easier
• Docker-machine create
– Creates a docker compatible cloud instance
– Works with many cloud providors
• Docker swarm:
– Clustering for docker containers

12. Example use cases in bioinformatics
• Software comparision
– http://nucleotid.es/assemblers/
• Illumina Basespace
– Uses docker for native apps
• Docker for reproducible research:
– http://arxiv.org/abs/1410.0846
• Solves “Dependency hell”
• Analysis pipelines (nextflow.io)