If you would like to look at a book I suggest:
    www.tldp.org/LDP/Bash-Beginners-Guide/Bash-Beginners-Guide.pdf

HOME

By default your HOME directory is the directory in which you "land" when you log in. The path of this directory is usually:
     /home/username
It is also stored in the HOME environment variable (see further down):
     echo $HOME

In general there is not much space in your HOME but therefore, at UQAM, a backup of everything you keep under your HOME is done every 3 hours. We also keep daily and weekly backups for up to 4 weeks. You if you ever remove something by accident or if the machine or disk unit crashes, there will still be a copy of everything you had in your HOME.
Therefore, it is strongly suggested that you keep everything which is small and important in your HOME! Like programs, scripts, configuration files.

Check out the following link to find out how to retrieve data from the home backup.

Shell

A shell is a UNIX system command processor. Basically, it is a command language to tell the system what to do. There are two major shell (command interpreter) families: 
    Bourne, Korn, Bash Shell
    C Shell
   
The syntax of shell commands can vary from one shell to another.
At UQAM we use the Bourne Again Shell (bash). Therefore all commands below are bash commands.

Syntax of a shell command

        command-name [ -option(s) filename(s) or arguments ]

Everything in square brackets [] is optional.

Example: ls -l filename

...

      ls -l -t -r
is the same as
      ls -lrt

In case you have a file name or an argument starting with a '-' you can use '--'. The command will NOT interpret anything following a '--' as an option/key.
For example if you are using 'grep' to look for '-a' in a file you could type:
    $  grep -iw -- -a filename

For more detailed explanations about Program Argument Syntax Conventions, please click on the here.

Documentation of specific commands - man & whatis

      whatis command    - displays a one-line summary about command
      man command         - displays on-line manual pages about command

'man' can be use on almost all of the shell commands listed below to get the complete description of the command.
To quit 'man' press 'q'.

Shell commands are case sensitive

Type commands exactly as shown; most shell commands are lower case. File and directory names can be lower, upper, or mixed case but must be typed exactly as listed.

Most important shell commands

...

Wild cards

Wildcards

Wildcards are "place holder" for one or many characters. A number of characters are interpreted by shell before any other action takes place. These characters are known as wildcard characters. Usually these characters are used in place of filenames or directory names.

Here are some examples for the usage of wild cardswildcards:

• cat c* : displays any file whose name begins with c including the file c, if it exists.
• ls *.c : lists all files that have a .c extension.
• cp ../rmt? .  : copies every file in the parent directory that is four characters long and begins with rmt to the working directory. (The names will remain the same.)
• ls rmt[34567] : lists every file that begins with rmt and has a 3, 4, 5, 6, or 7 at the end.
• ls rmt[3-7] : does exactly the same thing as the previous example.
• ls ~ : lists your home directory.
• ls ~username : lists the home directory of the guy with the user name username.

...

      echo "message" : displays/prints 'message'.

Examples:
     echo Hello
        Hello
     echo "Hello there"
        Hello there

...

printf

      printf : produces  produces output  according to a format.

...

      history : lists the most recent commands

Exit/Close a terminal or

...

process (script, command)

The easiest way to exit a script/process is by pressing the keys Ctrl-c.
The easiest way to close a terminal is by pressing the keys Ctrl-d.

...

'\' prevents the following character from being "interpreted". There are several "special characters" (see above) in shell which have a certain "meaning" and functions function as little "commands".
Unfortunately '\' has different meanings depending on where/how it gets used.
Examples:
    $  person=Alex
    $  echo $person
    Alex
    $  echo \$person
   

Examples:
      person=Alex
      echo $person
          Alex                     => Evaluation done !!!
      echo \$person
          $person              => No evaluation done !!!
    $  - Because of the back slash
      echo "\$person"
              $person              => No evaluation done !!!
    $  - Because of the back slash
      echo '\$person'
    Alex                             $person              => Evaluation No evaluation done !!!
- Because of the single quots

When used as the very last character in a line it will surpress suppresses the "new line".
    $

Command I/O

      >   :command output redirection (create new)
      >> : command output redirection(append)
      <   :command input redirection (from file)
      << : command input (from script or standard input)

Example:

...

...

...

...

...

...

null device

/dev/null or the null device is a special "file" that discards all data written to it but reports that the write operation succeeded.

File Operations

Search for Patterns in Files

      grep  search-string filename(s) : to find and type out lines containing the string in a file

Most useful search options:
    -i   : case insensitive search
    -w : whole words only
    -v  : invert match; type out lines that do NOT contain the string (invert the search)
    -c  : count the number of lines that contain a match

Search for files & directories

      find directory-name [-name (part_of_)name]

Useful for finding particular files or directories. 'find' descends the directory tree beginning at directory-name and locates files/directories that meet the search criteria
'find' is a very powerful and useful command. Use 'man find' to find out more.

Most useful search options:

For example, it can

Command I/O

...

null device

...

File Operations

Search for Patterns in Files

...

Search for files

find pathname -name search-string
Useful for finding particular files. find descends the directory tree beginning at each pathname and locates files that meet the specified conditions. Wild cards can be used in the search string.
find is a very powerful and useful command. Use 'man find' to find out more.
It can for example also be used in combination with 'grep':
    $
     find . -name '*.scrsh' -exec grep case {} \;

The above command will print all lines containing the word 'case' of files with end on '.scrsh'.

Counting words/lines/characters in a file

      wc filename(s) : counts the number of words, lines, and characters in a file
Options
Most useful search options:
          -l   : count lines lines
          -c  : count characters characters
          -w : count words words

Pipe

      | : (pipe) redirect standard output of first command to standard input of second command

Example:
    $   ls -1 | wc -l : count the number of files in a directory

Compare files

      difffilename1 filename2    : compares contents of two files on a line-by-line basis

      xxdiff filename1 filename2 [filename3]  : graphically compares contents of two or three files on a line-by-line basis. Can also be used to edit files!
      xxdiff directory1 directory2    : graphically compares contents of two directories
xxdiff can also be used to edit files!

      tkdifffilename1 filename2    : graphically compares contents of two files on a line-by-line basis. Use on guillimin onstead of 'xxdiff'.

File Transfer

File Transfer

While 'cp' can only be used to copy files and directories on the same machine, there are tools that can copy files and directories from one machine to another.

rsync

'rsync' stands for remote sync. It is a remote and local file and directory synchronization tool.

Examples:
rsync : a fast, versatile, remote (and local) file/directory-copying tool
Usage:
        rsync  origin  destination
      rsync  user@origin username@remote_origin_machine:origin  destination
      rsync  origin  user@destination  origin  username@remote_destination_machine:destination
'origin' and 'destination' can be file(s) and/or directories.
Only the origin or the destination machine can be a nother machine, not both.
Options:

...

files and/or directories.

Only either the origin or the destination machine can be another machine, not both.
The 'username@' only needs to be given for the remote machine and only if the username is different from the one on the local machine.
The default directory on the remote machine is the home directory. If the remote file/directory is not in the home directory a path need to be specified, either from the home directory or a full path.

Most useful options:

scp

scp : secure copy (remote file copy program)

Usage: similar to rsync aboveOptions

Most useful options:

ftp / sftp

Also see:
sftp : secure file transfer program
ftp : Internet file transfer program

wget

wget : web downloader
GNU Wget is a free utility for non-interactive download of files from the Web.

Example:
    $        wget www.tldp.org/LDP/Bash-Beginners-Guide/Bash-Beginners-Guide.pdf

File archiving and compressions

tar

"Tape archive" : tape archive, can create, add to, list, and retrieve files form an archive file (a collection of files or even whole directory trees archived together as one file).Options:

Most useful options:

Examples:
Create     Create       tar-file:      tar -cvf   cvzf  tar-filename.tar  filenames_to_archive
    Unarchive tar-file:   tar -xvf   xvzf  tar-filename.tar

gzip

...

/ gunzip

Compress : compress resp. expand files.

    gzip gzip      filename         :      compresses the file filename. Whenever possible, each file is replaced(!) by one with the same name and the extension .gz
    gunzip filename.gz   : uncompresses the gz-file again.
Good to save space!

zip

...

/ unzip

Package : package and compress resp. unarchive and uncompress (archive) files and directories.

    zip      zip-file.zip file file/directory_list  : archives and compresses all files/directories in file_list into zip-file.zip. Leaves original files untouched.
    unzip zip-file.zip                                      : unarchives and uncompresses all files/directories in zip-file.zip.
    unzip zip-file.zip aaa filename                   : unarchives and uncompresses only file 'filename' aaa fromzip-file.zip. Wildcards can get used.

Cursor movements in command line

emacs mode:   

...

...

...

...

...

...

...

...

...

Conditional structures

if-then-else

...

'elif expression ; thenelif' and 'else' are optional!!!expressions can look like this

Example 'expressions':

Arithmetic expression examples ( a=2 ): 
    (( a == 3 )) 
    (( b != 3 ))
    (( $a >= 3 ))
In Arithmetic expressions '(( ... ))' it is not necessary to put the '$' infront in front of variables since strings are not allowed so all strings are assumed to be variables anyways.

String expressions examples ( abc="Bonjour" ):
equal:
    [[ "$abc" == "Hello" ]]
not equal:
    [[ "$abc" != "Hello" ]]

The more common but less recomended recommended way is:
    [ $a -le 3 ]
resp.
    [ "$abc" -nq "Hello" ]

Note: It is mandatory to keep a 'space' just before and after the double and single square brackets!!!

and: &&
or: ||

If you want to know more about the comparison operators try:
    $      man test
or
    $      man bash            -> CONDITIONAL EXPRESSIONS

case-statement

A case statement is a conditional control structure that allows a selection to be made between several sets of program statements. It is a popular alternative to the if-then-else statement when you need to evaluate multiple different choices.

...

...

...

The pipe character '|' serves here as an "or".
The last line of each statement needs to be finished with ';;' at the end.

Examples:

...

...

...

...

...

...

Loops

Loops can be used to execute (parts of) code repeatedly.

for-loop

Loop over different fixed elements

...

...

Examples:

Loop over numbers:

...

Loop over files:

while-loop

Repeat statement(s) while 'condition' is true.

...

Example:

You One can also use a while-loop to read lines from an ASCII file.
Example:

...

...

...

break

...

& continue

To interrupt a loop you can use 'break' and 'continue'.
      break       interrupts the loop
      continue interrupts the current cycle of the loop

Manipulating Variables

Example string:
     $       string="ABC_abc_123"String

Get string length:

     $       echo ${#string}

Remove patterns from string

...

...

...

...

...

...

Look at these examples and you will understand the meaning of the above:
    $      string="ABC_abc_123"
    $      echo ${string#*_}     
             abc_123                                             123                                           => removes everything before first occurance of '_'
    $      echo ${string##*_}
             123                                                    => removes everything before last occurance of '_'
    $      echo ${string%_*}
             ABC_abc                                            abc                                          => removes everything after last occurance of '_'
    $      echo ${string%%_*}
             ABC                                                   => removes everything after first occurance of '_'
    $      echo ${string:s:n}
             abc                                                    => gets n characters, starting from position s

cut

Cut out/print part of the content of a variable:
cut prints selected parts of a string.
Options
Most useful options:

Examples:
    $      abc="I am hungry"
    $      echo $abc | cut -c 6-9
             hung                                                => returns characters 6-9
    $      echo $abc | cut -c 6-
             hungry                                            => returns characters 6 to end
    $      echo $abc | cut -d' ' -f 3
             hungry                                            => returns 3rd element with ' ' used as seperator
    $    abc="I am hungry. Are you?"
    $      echo $abc | cut -d. -f 2
              Are you?                                        => returns 2nd element with '.' used as seperator

set

When you call calling set without options but with one or more arguments, it sets the values of the command line argument variables ($1-$9$n) to its arguments.
Examples:
    $      abc="I am hungry"
    $      set $abc
    $      echo $3
             hungry

When options are specified, they set or unset shell attributes.
Options:

For more options check man page: man set
Examples:
    $      abc="I am hungry"
    $      set -x
    $      abc="I am hungry"
      + abc='I am hungry'

& -> Send job in background

You can send a job in the background by adding a '&' at the end of the command line.
This is useful to get the prompt back - beeing being able to continue using the window - when calling a program whic which opens a nother another window, like for example Matlab, emacs, xrec.
Example:
    $ matlab      emacs &

In case you forgot to add the '&' you can still send an already launched job into the background with 'Ctrl-z' followed by 'bg' (for background):
Example:
    $      emacs
         Ctrl-z
            [1]+  Stopped                 emacs
    $ bg
         bg
        [1]+ emacs &

Check and kill running processes

ps reports a snapshot of the current processesOptions

Most useful options:

Try for example:
     ps -fu $USER

Since the lines can get pretty long you can also pipe the output into less to see the full lines, for example:
    $      ps -fu $USER | less

Also have a look at the 'STIME' to see how old the processes are.

If ever you need to kill one of these jobs you can use 'kill' followed by the process ID, 'PID' (second column).
If a normal 'kill' does not work try 'kill -9' followed by the 'PID'.:
    kill -9 PID