Welcome to Introduction to the Unix Shell from fredhutch.io! This course introduces you to basic tasks using the Unix shell, including:
- working with files and directories
- combining commands using pipes
- repeating commands using for loops
- searching files and their contents
- retaining commands for reuse with shell scripts
- customizing your shell
A solid understanding of these basic principles is required prior to tackling material in our intermediate high performance computing (HPC) courses for both the on-premise clusters and cloud computing.
By the end of this lesson, you should be able to:
- viewing files and directories
- navigating paths
- combining commands with pipes
Check software installation
GUIs vs CLIs
command prompt
zsh vs bash https://stackabuse.com/zsh-vs-bash/ https://www.howtogeek.com/362409/what-is-zsh-and-why-should-you-use-it-instead-of-bash/
bash vs zsh
First command: username?
whoami
Next command: where am I in my computer?
pwd
What things are in this place in my computer?
ls
Change working directory to Desktop:
cd Desktop/
Download project directory
Download project:
On Linux:
wget https://raw.githubusercontent.com/fredhutchio/unix_shell_intro/master/example_unix_project.zip
On Mac:
curl https://raw.githubusercontent.com/fredhutchio/unix_shell_intro/master/example_unix_project.zip -o example_unix_project.zip
Unzip project, then inspect the project directory:
unzip example_unix_project.zip
ls example_unix_project
Describe project
- why a project?
- file and directory organization
relative vs absolute paths
. and ..
flags
ls -F
Do spaces matter?
ls -a
Relate to Fred Hutch drives
mkdir doc
cd doc
nano notes.md
mv
cp
rm
rmdir
wildcards
manuals, help
wc
redirection
cat
sort
pipes
head
options with values
what to do if I get stuck?
make sure work is saved
review how to get back into work
review objectives
preview next class's objectives