Linux is an operating system widely used in scientific computing including bioinformatics.
We will use the Introducing the Shell materials from the Data Carpentry Genomics workshop as an introduction to the shell. These materials were produced by The Carpentries, an international capacity building network focused on foundational coding and data science skills.
We have set up an environment providing web-based access to a small computer cluster at cluster.sanbi.ac.za. To log in to this environment, get a username and password from one of the trainers.
The machine that you will access is the “head node” of a cluster of three computers. When using a computer cluster you, the “head node” or “login node” is used for accessing the cluster but not for running data analysis. We will, however, use this computer for our introduction to the shell before switching over to the more powerful “worker node” computers of the cluster when doing bioinformatics.
The Software Carpentries Intro to the Shell lesson covers a lot of the same commands used in the lesson we have provided, but with a slightly different focus and different data.
Sandbox.bio provides a shell that runs in your browser along with a series of lessons on command line bioinformatics.
The Galaxy Training Network “Foundations of Data Science” training provides a lesson on CLI basics that can be run in an Interactive Environment on the usegalaxy.eu server.
If you want to know more about Linux commands, consult this Linux command reference.
And more Bash Learning Resources from Microbiome binfies.