The Command Line Interface (CLI)

The CLI provides a direct way to interact with the Operating System, by typing in commands.

Why the CLI is worth learning

Might be the only interface you have to a High Performance Computer (HPC)
Command statements can be reused easily and saved as scripts
Easier automation and text files manipulation

A little bit of terminology

Command Line Interface (CLI): This is a user interface that lets you interact with a computer. It is a legacy from the early days of computers. Now a days computers have graphical user interfaces instead (MacOS, Windows, Linux, …).
Terminal: It is a an application that lets you run a command line interface. It used to be a physical machine connected to a mainframe computer
Shell: It is the program that executes the commands you pass via the command line interface. There are many different shells, the most common being bash (Bourne Again SHell) which is installed by default in many Linux distributions, although zsh, often seen a more features full (here), has become the default shell on MacOS.

The pitch

Not convinced? Check this out: the CLI pitch

The Terminal from RStudio

You can access the command line directly from RStudio by using the Terminal tab next to your R console.

Navigating and managing files/directories in *NIX

pwd: Know where you are
ls: List the content of the directory
cd: Go inside a directory

Some pseudo directory names. Wherever you are:

~ : Home directory
. : Here (current directory)
..: Up one level (upper directory)

Let’s put this into action:

go to my “Home” directory: cd ~
go up one directory level: cd ..
list the content: ls
list the content showing hidden files: ls -a note that -a is referred as an option (modifies the command)

More files/directories manipulations:

mkdir: Create a directory
cp: Copy a file
mv: Move a file it is also how you rename a file!
rm / rmdir: Remove a file / directory use those carefully, there is no return / Trash!!

Note: typing is not your thing? the <tab> key is your friend! One hit it will auto-complete the file/directory/path name for you. If there are many options, hit it twice to see the options.

Permissions

All files have permissions and ownership.

List files showing ownership and permissions: ls -l

brun@workbench-1:/courses/EDS214$ ls -l
total 16
drwxrwxr-x+ 3 brun      esmdomainusers 4096 Aug 20 04:49 data
drwxrwxr-x+ 2 katherine esmdomainusers 4096 Aug 18 18:32 example

You can change those permissions:

Change permissions: chmod
Change ownership: chown

Tip

Clear contents in terminal window: clear

General command syntax

command [options] [arguments]

where command must be an executable file on your PATH * echo $PATH

and options can usually take two forms * short form: -a * long form: --all

You can combine the options:

ls -ltrh

What do these options do?

man ls

Tip

hit spacebar to get to the next page of the manual hit q to exit the help

Getting things done

Some useful, special commands using the Control key

Cancel (abort) a command: Ctrl-c Note: very different than Windows!!
Stop (suspend) a command: Ctrl-z
Ctrl-z can be used to suspend, then background a process

Process management

Like Windows Task Manager, OSX Activity Monitor
top, ps, jobs (hit q to get out!)
kill to delete an unwanted job or process
Foreground and background: &

What about “space”

How much storage is available on this system? df -h
How much storage am “I” using overall? du -hs <folder>
How much storage am “I” using, by sub directory? du -h <folder>
How much RAM is used? free -h

Existential questions

What is your username? whoami
What is today’s date? date
Where are the programs you are using? whereis R also try which -a python
What is the kernel version of your OS: uname -a
How long since last reboot: uptime
Which shell are you using? echo $0

History

See your command history: history
Re-run last command: !!
Re-run 32th command: !32
Re-run 5th from last command: !-5
Re-run last command that started with ‘c’: !c

A sampling of simple commands for dealing with files

wc count lines, words, and/or characters
diff compare two files for differences
sort sort lines in a file
uniq report or filter out repeated lines in a file

Get into the flow, with pipes

http://www.ucblueash.edu/thomas/Intro_Unix_Text/Images/pipe_split.png — `stdin`, `stdout`, `stderr`

wc -l *.TXT 
wc -l *.TXT | sort -n

note use of * as character wildcard for zero or more matches (same in Mac and Windows)
? matches single character;

Here the wc -l command, which counts the number of lines in files, is given file names on the command line, so it counts the lines in those files. It writes its output to stdout. sort -n sorts lines in files. It was given no files to sort, so it sorts whatever lines come in via stdin. By piping these together (i.e., by hooking wc’s stdout to sort’s stdin using the pipe operator), the output from wc -l is thereby sorted.

There are various operators for redirecting where stdin comes from and where stdout and stderr go:

< file: read stdin from file
> file: write stdout to file
2> file: write stderr to file
>& file: write both stdout and stderr to file
>> file: append stdout to file

Let’s write the above result to a file:

wc -l *.TXT | sort -n > csvcount.log

Caution: except for >>, all forms of > are destructive: Bash overwrites any existing file with an empty file before the program is run.

Want to get rid of output you don’t want to see? Use the Unix black hole: >& /dev/null. (This is a cultural meme, you’ll see it on T-shirts and license plates.)

The above are the main redirections, but there are others.

To end a session, simply type exit or logout into the command line

Setting git on workbench-1 (if not yet done)

At the Terminal:

git config --global user.name "Jane Doe" 
git config --global user.email janedoe@example.com
git config --global credential.helper 'cache --timeout=10000000'
git config --list

Setting GitHub token on workbench-1

At the R Console:

# On your laptop
usethis::create_github_token() # This should open a web browser on GitHub

# On workbench-1 
gitcreds::gitcreds_set()
usethis::git_sitrep()

CLI Practice

Bonuses

Hear more about the UNIX revolution directly from its creators

https://www.youtube.com/watch?v=tc4ROCJYbm0

Vim text editor

This section is optional depending of our progress and interest. Vim is still the default text editor on many Linux distribution and it is good to know about its basics.

Vim

Advanced CLI

Want to know more cool tools your can use: CLI Advanced

Acknowledgements

This section reuses materials from NCEAS Open Science for Synthesis (OSS) intensive summer schools and other training. Contributions to this content have been made by Mark Schildhauer, Matt Jones, Jim Regetz and many others; and from EDS-213 10 bash essentials developed by Greg Janée.