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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