The Command Line Interface Shell - clizarraga-UAD7/Workshops GitHub Wiki
The Command Line Interface is the standard way of interacting thru a shell (command line interpreter) with an Operating System (UNIX, Linux, MacOS,and others). There are several shell options in the Unix/Linux systems environments, which are used in diverse applications:
- Bourne Shell - /bin/sh
- Bourne Again Shell - /bin/bash - Most used by default.
- C Shell - /bin/csh
- Debian Almquist Shell - /bin/dash
- Korn Shell - /bin/ksh
- Tcsh - /bin/tcsh
- Z shell - /bin/zsh
Many Linux systems users use /bin/bash, that comes configured by default. To find out which shell you are using in a terminal session type: echo $SHELL.
The Shell or command line interpreter, is the intermediary between the user and the operating system. It interprets what we type. If the typed command is not recognized by the interpreter it will generate a warning or help us complete the posible commands.
It's possible to change the Shell program, simply we can run a Shell on top of another. To finish a user session in that Shell, we type exit.
Most shells are equivalent, they have many characteristics in common. The differences are noted when we try to write Sell command scripts, called Shell Scripting which is done to automate repetitive tasks.
There are several options to access a CLI on a local computer:
- Linux Terminal that is included in every Linux system.
- MacOS Terminal included in every MacOS system, under Applications/Utilities.
If the previous local options are not available, there are cloud accessible CLI options:
- Github Codespaces, requires a Github account.
- Google Cloud Shell, requiring a Google account.
- Cyverse Cloud Shell for CyVerse users.
- UA HPC Interactive Desktop, for UA HPC users.
Codespaces terminal within VSCode is a pre-configured, cloud-based, efficient, secure, and easy-to-use environment that is integrated with VSCode and uses a virtual machine, making it accessible from anywhere and requiring less resources on the user's computer.
(Image credit: Author, CC)
Google offers a Shell for a Command Line Interface. We can connect to it using a Google Account via a Web Browser. Recommended browsers are Firefox, Google Chrome, but does not exclude others (?).
The URL for launching a Google Cloud Shell is: https://shell.cloud.google.com
(You can watch an Introduction to Google Cloud Shell in this 6 min video by Diane K. Patterson).
Also, it is important that you read this Basic Tutorial about Google Cloud Shell Setup by Dianne K. Patterson.
(Image credit: Author, CC)
If you are a CyVerse user, you can launch a CLI Cloud Shell instance, via the Discovery Environment Dashboard, under Apps, and then access it thru the Analyses option. This is an Ubuntu Linux terminal.
When you are done, type exit in the terminal, and then go to Analyses, select the running Cloud Shell and go to More actions and Terminate the Shell.
(Image credit: Author, CC)
If you are a UA HPC user, then you can access via web the ood.hpc.arizona.edu dashboard and request an Interactive Desktop, that offers you a virtual Centos 7 Linux system. Use the default values, specify your HPC group and launch the instance. You may need to wait in the queue, until the Desktop is ready and open it.
When you are done, you can select System/Shutdown the Interactive Desktop.
The command line interface (CLI) or Shell, is inherited from the UNIX shell, and it includes a family of user and system administration commands.
In the following table we present a minimum set of commands to get started.
| Command | Description |
|---|---|
man command1 |
Show manual entry for command1
|
command1 --help |
Will show the syntax on how to use command1
|
apropos keyword |
Search the manual pages and descriptions that include keyword
|
pwd |
Present working directory |
cd |
Change to directory |
cd or cd ~
|
Change to Home directory |
cd .. |
Change to parent directory |
cd - |
Change to previous visited directory |
ls -al |
List all files in directory |
ls -alR |
List all files recursively |
cat file1 |
Concatenate file1 and display contents to screen |
cat file1 file2 > file3 |
Concatenates files1 and file2 and writes to file3
|
cat file4 >> file3 |
Appends file4 contents to existing file3
|
cp |
Copy files and directories |
cp file1 dir1 |
Make a copy of file1 into directory dir1
|
cp -r dir1 dir2 |
Copy recursively directory dir1 into directory dir2
|
mv |
Rename files |
mv file1 new_file |
Renames file1 to new_file
|
rm |
Remove or delete files (Use with Caution) |
rm file1 |
Removes file1 permanently |
rm -r dir1 |
Removes the directory dir1 and all its contents permanently |
rmdir |
Removes an empty directory |
history |
Show command line history |
clear |
Clear the terminal screen |
touch newfile |
Create an new empty file if it does not exist |
head -n 5 filename |
Show the first 5 lines of a file |
tail -n 5 filename |
Show the last 5 lines of a file |
more filename |
Show the contents of a file, one page at a time in the forward direction (SPACE BAR). Type 'q' to quit. |
less filename |
less is opposite of more. Show the contents of a file, one page at a time, forward (SPACE BAR) and backward ('u'). To end of file ('G'), and beginning of file ('p'). Type 'q' to quit. The manages uses less`to show the manual contents. |
wc filename |
Prints number of lines, words and characters in a text file |
find ./ -name 'a*.txt' -print |
To search for files in the file hierarchy |
Other useful commands
| Command | Description |
|---|---|
echo |
Display a line of text |
echo abcd > file1 |
Echo abcd and write to file1
|
echo $SHELL |
Display the value of the SHELL variable |
echo $PATH |
Display PATH environment variable |
file |
Return the type of file |
tar cvf dir1.tar dir1 |
Archive a whole directory and contents |
tar xvf dir.tar |
Will unarchive tar file and restore its contents and directory structure |
gzip file.tar |
Will produce compressed file.tar.gz
|
gunzip file.tar.gz |
Will uncompress file and return file.tar
|
The UNIX/Linux Shell handles special symbols:
`~` the Home directory
`.` the current working directory
`..` the parent directory
`*` wildcard that matches any character
`?` wildcard that matches exactly one character
TAB will autocomplete command/filename, given initial sequence of characters
One of the advantages of working with these Shells is that, they inherit the some editing commands from the GNU Emacs Editor. This allows us to move our cursor to move and "edit" the command line text.
For completeness we summarize these commands, because we will be using them extensively:
| Command | Action |
|---|---|
| Positioning | |
Ctrl+f |
Moves the cursor one character forward |
ESC, f
|
Moves the cursor one word Forward |
Ctrl+b |
Moves the cursor one character backward |
ESC, b
|
Moves the cursor one word Backward |
Ctrl+a |
Moves the cursor to the beginning of line |
Ctrl+e |
Moves the cursor to the end of line |
Ctrl+p |
Moves the cursor to the previous line in commands history |
Ctrl+n |
Moves the cursor to the next line in commands history |
| Memory buffer | |
Ctrl+k |
Sends contents of right region after cursor to memory (a.k.a. Kill. Memory keeps only last contents if overwritten) |
Ctrl+y |
Flushes the contents in memory into cursor position (a.k.a. Yank) |
Having these commands in mind, will ease our job of command line editing when needed.
Also, take advantage of the word completion capability offered by the Shell, for example in the case of long file/directory names.
| Command | Description |
|---|---|
chown username filename |
Change ownership of a file |
chgrp group name filename |
Change group name of a file |
chmod +x filename |
Making a file executable |
or chmod 755 filename
|
📝 More on file permissions: Click to expand!
When executing a list file command: ls -al, a list of 10 characters (octal bits) will appear at the beginning of a line.
drwxr-xr-x 5 user group 160 Oct 11 09:37 dir1
-rw-r--r-- 1 user group 7080 Apr 15 19:20 TheRaven.txt
-rwxr-xr-x 1 user group 92 Oct 11 09:54 script.sh
they are related with file type and permissions.
- The first character defines if it is a directory ('d'), or an ordinary file ('-').
- The next 3 characters (2nd thru 4th), defines if the user has permissions to read it ('r'), write or modify it ('w'), and execute it ('x'). A missing permission is denoted by the empty character ('-').
- The following 3 characters starting at the 5th one, defines the permissions to the group the user belongs to.
- The last 3 characters starting at the 8th place defines the permissions to other (the rest of the world).
To turn on/off the permission octal bits, use the chmod command.
Numeric octal bits (0-7):
7 = 2^2 + 2^1 + 2^0 = 4 + 2 + 1 -> ('rwx')
6 = 2^2 + 2^1 + 0 = 4 + 2 + 0 -> ('rw-')
5 = 2^2 + 0 + 2^0 = 4 + 0 + 1 -> ('r-x')
4 = 2^2 + 0 + 0 = 4 + 0 + 0 -> ('r--')
0 = 0 + 0 + 0 = 0 + 0 + 0 -> ('---')
Examples
- Text files:
chmod 644 filename, gives 'rw' permission to owner, 'r' permissions to the group and other ('-rw-r--r--') - Text files:
chmod 600 filename, the owner has 'rw' permissions. No one else can read, write or execute that file. - Executable file:
chmod 755 filename, gives 'rwx' permissions to owner, 'r-x' permissions to the group and other ('-rwxr-xr-x') - Executable file:
chmod 700 filename, the owner has 'rwx' permissions. No one else can read, write or execute that file.
In UNIX/Linux files and directories are equivalent. In the case of a directory: 'r' means you can read the contents of a directory, 'w' means you can create/delete files in that directory and 'x' means you can enter into a directory.
By default, the system will create directories with '755' permissions and regular files with '644' permissions.
chmod 000 filename. You will deny all 'rwx' permissions to yourself and everyone else.
| Command | Description |
|---|---|
exit |
Finish user session in terminal |
Ctrl-C |
Abort job execution |
Ctrl-Z |
Suspend job execution |
jobs -l |
List jobs of current session |
fg %Number |
Run job in foreground |
ps ax |
List system processes |
ps u |
List user processes |
program & |
Execute program in background |
| `kill -9 PID | Terminate process with ID number |
kill %1 |
Will kill the first process in background mode (use jobs -l to list jobs) |
w |
Show who is connected and what process is running, uptime, CPU load |
who |
Show who is logged in |
top |
Show top processes running |
printenv |
Prints user environment variables |
| Command | Description |
|---|---|
df -h |
Available system disk space, human readable |
du -h |
Approximate disk use of current directory, human readable |
cal 10 2022 |
Displays a calendar for October 2022 |
date |
Displays system date and time |
bc -il (ENTER) |
Arbitrary precision calculator |
If you need to create/edit/modify a text file or source code, most systems include a family of basic editors.
Please explore the possible text editors included in your system:
- vim text editor: vim help | vim 101. Vim is a free and open-source, screen-based text editor program.
- pico text editor: pico editor manual. Pico is a text editor for Unix and Unix-like computer systems.
- GNU nano text editor: Nano documentation. GNU nano is a small and friendly text editor. Nano emulates the Pico editor.
- Emacs : Basic Emacs | Emacs HowTo. Emacs or EMACS is a family of text editors that are characterized by their extensibility.
- Atom text editor | Atom basics. Atom is a free and open-source text and source code editor for macOS, Linux, and Microsoft Windows with support for plug-ins written in Node.js, and embedded Git Control, developed by GitHub.
- Visual Studio Code | Docs. Visual Studio Code, also commonly referred to as VS Code, is a source-code editor made by Microsoft for Windows, Linux and macOS. Features include support for debugging, syntax highlighting, intelligent code completion, snippets, code refactoring, and embedded Git.
Online Help
- Explain Shell. Explains a Linux command.
- Online Linux Man Pages. Man7.org.
- Linux Commands Cheat Sheet. Option 1
- Linux Commands Cheat Sheet. Option 2
Other resources
- Introduction to Command Line for Bioinformatics. UC Davis Bioinformatics Core.
- Introduction to Linux. Augustine Abaris. Boston University.
- Neuro Imaging Workshop. Dianne K. Patterson, UofA
- UNIX Tutorial for Beginners. [email protected].
- UNIX Camp for Neuroimagers. Openclass.ai.. Dianne K. Patterson, UofA.
Created: 02/24/2022 (C. Lizárraga); Updated: 05/14/2023 (C. Lizárraga).
