Reproducibility in Computational Biology
Medical Microbiology Maastricht UMC
October 2nd, 2020
@ines_cim
cimendes
Inês Mendes
Containerization with Docker
Software Containers
| What is it?
In the Paleolithic era:
Virtual Machines
“Bare Metal” Installation
Software Containers
| What is it?
In the Modern days:
Software Containers
Software Containers
Runs the same regardless of the environment.
A container image is a lightweight, stand-alone, executable package of a software that includes everything needed to run it:
- code
- runtime
- system tools
- system libraries
| What is it?
Software Containers
| What is it?
Host Hardware
Host Hardware
Container Engine
Host OS
Host OS
Hypervisor
Guest OS
Guest OS
App
App
Guest OS
VM1
VM2
App
App
App
App
Virtual Machines
Containers
Docker
| Why Docker
Pros:
Cons:
- Fast and easy to set up
- Very well documented
- Has public container registries (DockerHub)
- Multi-platform support
- Support for container orchestration (DockerCompose)
- Poor Monitoring (3rd party tools)
- Requires sudo for installation & run (uDocker)
- Closed-Source & commercial
Docker
| Why Docker
Pros:
Cons:
- Fast and easy to set up
- Very well documented
- Has public container registries (DockerHub)
- Multi-platform support
- Support for container orchestration (DockerCompose)
- Poor Monitoring (3rd party tools)
- Requires sudo for installation & run (uDocker)
- Closed-Source & commercial
Almost all container software can deploy Docker Containers!
Docker Hub
build
pull & run
host
push
Docker
| The ecosysthem
Docker
| Resources
"Hands on" Demo!
