Advanced CLI in Galaxy

e-learning

View material

Abstract

This tutorial will walk you through the basics of how to use the Unix command line.

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Redirect a command's output to a file.
Process a file instead of keyboard input using redirection.
Construct command pipelines with two or more stages.
Explain what usually happens if a program or pipeline isn't given any input to process.
Explain Unix's 'small pieces, loosely joined' philosophy.
Write a loop that applies one or more commands separately to each file in a set of files.
Trace the values taken on by a loop variable during execution of the loop.
Explain the difference between a variable's name and its value.
Explain why spaces and some punctuation characters shouldn't be used in file names.
Demonstrate how to see what commands have recently been executed.
Re-run recently executed commands without retyping them.
Use grep to select lines from text files that match simple patterns.
Use find to find files and directories whose names match simple patterns.
Use the output of one command as the command-line argument(s) to another command.
Explain what is meant by 'text' and 'binary' files, and why many common tools don't handle the latter well.

Licence: Creative Commons Attribution 4.0 International

Keywords: Foundations of Data Science, bash, jupyter-notebook

Target audience: Students

Resource type: e-learning

Version: 11

Status: Active

Prerequisites:

CLI basics

Learning objectives:

Redirect a command's output to a file.
Process a file instead of keyboard input using redirection.
Construct command pipelines with two or more stages.
Explain what usually happens if a program or pipeline isn't given any input to process.
Explain Unix's 'small pieces, loosely joined' philosophy.
Write a loop that applies one or more commands separately to each file in a set of files.
Trace the values taken on by a loop variable during execution of the loop.
Explain the difference between a variable's name and its value.
Explain why spaces and some punctuation characters shouldn't be used in file names.
Demonstrate how to see what commands have recently been executed.
Re-run recently executed commands without retyping them.
Use grep to select lines from text files that match simple patterns.
Use find to find files and directories whose names match simple patterns.
Use the output of one command as the command-line argument(s) to another command.
Explain what is meant by 'text' and 'binary' files, and why many common tools don't handle the latter well.