itsjeffreyy / bio-workshop-18

Pawsey workshop: containers for bioinformatics

Hands-on workshop on Containers for Bioinformatics

Workshop GitHub Home: https://github.com/PawseySC/bio-workshop-18

Table of Contents

1. BLASTing from a container
2. Introducing Docker, repos, containers
3. Exploring a bioinformatics container
4. Containerising a WGS workflow
5. Porting to HPC systems
6. Building and running a Cellranger container
7. Building a basic RStudio image

Requirements

• A computer with a Unix-like terminal and Docker installed; creation of a free account might be required to Download Docker.
• Some knowledge of Unix-like terminals is recommended, including basic commands and text editors; a good learning resource can be The Unix Shell: Pawsey Edition.
• To optionally test the scripts in Episode 5 (HPC porting), access is required to a system where Shifter is installed.

Releases

• Fixes and improvements are being commited to the master branch of this repo
• 7Sep18 : Pawsey COMBINE Bioinformatics Symposium 2018, 6-7 Sep 2018
• 3Dec18 : AMSI BioInfoSummer 2018, 3-7 Dec 2018