Docker training

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The NGS Academy forms part of the Africa CDC Pathogen Genomics Initiative (PGI). This initiative is funded by the Bill & Melinda Gates Foundation. Our training initiatives are carried out in partnership with the African Society for Laboratory Medicine (ASLM).

Course overview:

In this course you will learn the fundamentals of Docker and containers from a bioinformatics perspective. First, you will learn what docker is, docker commands and alternatives to docker. Along the way, you will learn how to create Docker images and understand the concept of containers.

Intended audience:

Beginner - Intermediate level Bioinformaticians working with next-generation sequencing

Pre-requisite:

Docker installed

The course will cover:

Introduction to docker and docker commands
Docker alternatives
Docker containers

Logistics:

Venue of course: Online
Dates for the course: Self paced

Course curriculum:

What is docker?
Docker commands
Alternatives to Docker
Docker containers

Course schedule and Materials:

Day 1

Session	Course materials	Training partner	Interactive Sessions with Instructor/s
Session 1	Introduction to the Course 1. Introduction to Docker Containers Part 1	MRIGlobal	August Thomas
Session 2	2. Introduction to Docker Containers Part 2	MRIGlobal	August Thomas

Session	Course materials	Training partner	Interactive Sessions with Instructor/s
9:00am - 10:00am	1. Recap from yesterday 1.1 Introduction to docker mounts and volumes 1.2 Working with volumes and persisting data 1.3 Introduction to singularity	MRIGlobal	Dr Philip Ashton Dr George Githinji
10:30am - 1:00pm	2. Introduction to Git 2.1 Software carpentry (Basic Unix and Git)	MRIGlobal	Dr Philip Ashton Dr George Githinji
2:00pm - 3:00pm	3. File organisation. 3.1 Guide to organisation of Computational Biology projects 3.2 Mordern file organisation 3.2.1 Practical 1 3.2.2 Practical 2 3.2.3 Practical 3	KEMRI	Dr George Githinji

Session	Course materials	Training partner	Interactive Sessions with Instructor/s
9:00am - 1:00pm	1. Introduction to Snakemake 1.1 Scripting 1.2 Basic concerpts 1.3 Running a basic pipeline 1.4 Configurations 1.5 Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers	Malawi-Liverpool-Wellcome Trust KEMRI	Dr Philip Ashton, Belson Kutambe Dr George Githinji
2:00pm - 4:00pm	2. Running snakemake. 2.1 Run snakemake with conda 2.2 Running snakemake on HPC 2.3 Practical: Snakemake	Malawi-Liverpool-Wellcome Trust KEMRI	Dr Philip Ashton, Belson Dr George Githinji

Session	Course materials	Training partner	Interactive Sessions with Instructor/s
9:00am - 10:00am	1. Running Snakemate cont...	ILRI KEMRI Malawi-Liverpool-Wellcome Trust	John Juma Dr George Githinji Belson Kutambe
10:30am - 1:00pm	2. Sharing pipelines	Malawi-Liverpool-Wellcome Trust KEMRI ILRI	Dr Philip Ashton, Belson Kutambe John Juma
2:00pm - 4:00pm	3. Introduction to Bioinformatics workflows with Nextflow and nf-core 3.1 Advanced workflows (Nextflow and Common Workflow Language) (Nextflow Exercises) 3.2 Compare and contrast with Snakemake 3.3 Simple worklfows 3.4 Using docker in worklfows 3.5 Using HPC 3.6 Introduction to Common Workflow language (CWL)	ILRI KEMRI	John Juma Dr George Githinji

Session	Course materials	Training partner	Interactive Sessions with Instructor/s
9:00am - 1:00pm	Practical project on implementing your own workflow	KEMRI Malawi-Liverpool-Wellcome Trust	Dr George Githinji Dr Philip Ashton