Intro to CLI (Command Line Interface)

https://swcarpentry.github.io/shell-novice/

Why CLI?

The HPC has a limited graphical interface; getting the most out of the built-in functions will save you a great deal of frustration

man or -h/--help

...will bring up instructions for any that you’re trying to call.

Command line tutorials

http://linuxcommand.org/lc3_learning_the_shell.php

https://openclassrooms.com/en/courses/4614926-learn-the-command-line-in-terminal

Fundamentals

ls or ls

list information (what’s in this directory?)

cd or cd .. or cd

Change directory to path or up to parent directory or to ~/

mv

Move a file to another file

cp

Copy a file to another file

File manipulation

comm

Compare file 1 and 2, produce lines in common and unique to each file. File1 and 2 must be sorted first

sort

Sort file

head

Output first ten lines of a file (with -n option, output first n lines)

tail

Output last ten lines of a file (with -n option, output last n lines)

cat

Read /output contents of file

echo “”

Output text

Std I/O

<</>>

Ordinarily, standard input for a function come from/return to the terminal. You can redirect files in place of the terminal though.

echo “hello” >> hello

Chaining commands

Pipes! “|”

Redirects to a process, rather than a file. So you can chain together multiple commands.

cat seagate1.md5 | sed 's/[()]//g' | awk '{print $4,$2}' | sort > seagate_for_commm.md5

Shell variables

Say the magic $

One line magic

awk/sed/grep

for loops -

for/if/else/array loop structures

command editors

(vi/vim, emacs, nano)

shell tips & tricks

alias', .bash_rc, .bash_history, env’s