Using the Command Line

Welcome to the second lesson of our Metagenomics with High Performance Computing course.

In this lesson we will continue learning the foundational command line skills needed for metagenomics analysis. We will recap how to navigate our cloud-based file system, learn how to work with files and discover how combining commands can unlock new possibilities.

Getting Started

This lesson assumes no prior experience with the tools covered in the module. However, learners are expected to have some familiarity with biological concepts.

Participants should bring their laptops and plan to participate actively.

Before starting this lesson, you should make sure you have fully covered the Files and Directories lesson.

Schedule

00:00 1. Navigating Files and Directories How can I perform operations on files outside of my working directory?
What are some navigational shortcuts I can use to make my work more efficient?
00:50 2. Working with Files and Directories How can I view and search file contents?
How can I create, copy and delete files and directories?
How can I repeat recently used commands?
01:35 3. Redirection How can I search within files?
How can I combine existing commands to do new things?
02:20 Finish

The actual schedule may vary slightly depending on topics and exercises chosen by the instructor.