Intermediate Linux Command Line & Basic Scripting

Instructors

Marc Gouw, Jean-Karim Hériché

Course Description

This course will teach you the basis of the most powerful aspects of command line computing on Linux operating systems and other Unix environments such as Mac OS X. Knowing how to quickly and specifically access information from huge files, customise your working environment, and write scripts to make your analyses automated and flexible, is extremely valuable and powerful for modern biological research. The skills that you learn on this course could save you a huge amount of time in the future, as well as ensuring that your research is more reproducible by making it easy to maintain consistency across the analysis of many samples.

This course is aimed at users who have basic knowlege of Linux commands (man, cd, pwd, cp, rm, mkdir, cat, less, grep, head, ssh etc.), perhaps from attending the other Bio-IT course, “Introduction to Linux Command Line”.

The course runs over three consecutive mornings (3rd session optional), with material covering:

• advances methods for extracting and working with data from textfiles (gzip, tar, grep, cut, sort, sed, awk)
• setting and working with environment and shell variables
• the basics of script writing in bash

In the third (optional) part, we will provide time to put the lessons into practice in more extended exercises and to discuss the attendees’ own projects.

Script syntax will focus on bash.

Duration: 3 x 4 hours (third session optional)

Bookings