Introduction to Docker and Singularity

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introduction to docker and singularity

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Introduction to Docker 8 Topics

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Background about Docker

Docker components

Docker vocabulary

Container Setup explained

Basics of the Docker images

What is Containerization?

Advantages of Docker

Typical use cases

Using existing images 13 Topics

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Explore Docker hub

Exercise on getting images

Get tools from Biocontainers

List docker images

Starting an image with docker run

Run container as daemon

Check containers status via docker ps

Clean up the containers and the images

Execute a process in running container

Excercise with volumes

Docker recipes: build your own images 12 Topics

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Building the recipes for images

More advanced image building

Tagging the images

Starting the build

More instructions for the recipes

One tool, one image or some tools, one image

General recommendations

Dockerfile tips

Getting an image to Docker Hub

Inspecting Dockerfiles created by other parties

Using Biocontainers and Bioconda for bioinformatics tools

Introduction to Singularity 6 Topics

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Background about Singularity

Strengths and Weaknesses

Singularity Architecture

Getting started

Singularity’s Image Cache

Using existing Singularity images

Run and execute Singularity images 6 Topics

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Using the Singularity containers to run commands

Files in Singularity containers

Binding local folders (aka volumes)

Using Docker images with Singularity

Run from sandbox container or remotely

Troubleshooting options

Building Singularity images 4 Topics

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Building Singularity images

Change the image via sandbox

Using singularity recipes

Remotely building

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