This website is a companion reference for the corresponding BCC2020 conference session.
This workshop is designed for students who already have a basic familiarity with running programs and navigating the filesystem in a unix shell. It aims to refresh some of that basic knowledge and then build upon it to demonstrate powerful features of the shell that can be used to speed up common bioinformatics tasks.
Ira Cooke is a senior lecturer in bioinformatics at James Cook University and co-director of its Centre for Tropical Bioinformatics and Molecular Biology.
He is also occasionally active on twitter @iracooke
All the files you need to run the exercises should already be setup in your user account on rstudio.bioinformatics.guide
Terminalfeature provided by rstudio. Click
cd bcc2020cle wget -L https://raw.githubusercontent.com/iracooke/bcc2020CLE/master/setup.sh bash setup.sh
Start with this presentation which outlines why command line skills are important and runs through the key features of the Bash shell.