Files and Directories

A comic figure is looking over the shoulder of another and is shocked by a list of files with names like 'Untitled 138 copy.docx' and 'Untitled 243.doc'. Caption: 'Protip: Never look in someone else's documents folder'. — .

Welcome to the first lesson in Cloud-SPAN’s Metagenomics with High Performance Computing course!

Over the next two lessons we will cover the foundational skills and knowledge needed for the rest of the course. Once you are comfortable with these skills, we can move on to applying them to a metagenomics analysis workflow.

In this lesson we will learn how the files and directories on your computer are structured, as well as logging onto the cloud and using the command line (also known as the shell and the terminal) for the first time. It is heavily based on the first lesson of our Prenomics course.

By the end of this lesson you will be able to:

Explain the hierarchical structure of a file system.
Understand what working directories, paths and relative paths are.
Log onto to a running instance.
Navigate a file system using the command line.
Access and read help files for bash programs and use help files to identify useful command options.
Work with hidden directories and hidden files.

Getting Started

This lesson assumes no prior experience with the tools covered in the module. It is designed for absolute beginners.

This lesson uses an Amazon Web Services (AWS) instance, which is a Linux virtual machine. Your AWS instance will be created for you and you will be sent the log in information you will need for this lesson.

Before starting you should read the Precourse Instructions page.