1. Unix and shell commands — unix tutorial 0.1 documentation (2024)

See also

for geting help from the shell, use man, e.g.

• man tcsh
• man bash

1.1.1. bg¶

put the most recently accessed job (child process) in the background

This is most commonly entered after ctrl-z. One might also use the output of jobs, and specify a job number.

1.1.2. cd¶

change directories

The cd command is used to change directories. Without any parameters, the shell will change to the user’s home directory ($HOME). Otherwise, it will change to the single specified directory.

Examples:

cdcd $HOMEcd suma_democd AFNI_data6/FT_analysiscd ~usernamecd /absolute/path/to/some/directorycd relative/path/to/some/directorycd ../../some/other/dir

Since .. is the parent directory, including such entries will travel up the directory tree.

1.1.3. echo¶

echo text to the terminal window

The echo command displays the given text on the terminal window. This is often used to show the user what is happening or to prompt for a response. There are more devious uses, of course...

Examples:

echo hello thereecho "this section performs volume registration"set my_var = 7echo "the value of my_var = $my_var"

1.1.4. fg¶

put the most recently accessed job (child process) in the foreground

This is most commonly entered after ctrl-z. One might also use the output of jobs, and specify a job number.

While bg keeps a process running, but leaves the terminal window available for new commands, fg puts a process in the foreground, so commands would no longer be available.

See also: bg

1.1.5. jobs¶

list processes started from current shell

The jobs command lists processes that have been started from the current shell (the current terminal window, probably) that are either suspended or running in the background. Processes are suspended via ctrl-z, and can then be put into the background using the 'bg‘ command (or by using & in the first place).

Examples:

jobs - probably shows nothing

1.1.6. set¶

assign a value to a shell variable

The set command assigns a value to a variable (or multiple values to multiple variables). Without any options, all set variables are shown.

If a value has spaces in it, it should be contained in quotes. If a list of values is desired, parentheses () should be used for the assignment, while indivisual access is done via square brackets [].

Examples:

setset value = 7set new_val = "some number, like seven"echo $new_valset list_of_vals = ( 3 1 4 one five )echo $list_of_valsecho $list_of_vals[3]set path = ( $path ~/abin )

1.1.7. setenv¶

set an environment variable

The setenv command works like ‘set’, except that if a child shell is started (such as when running a script), the environment variables are preserved. Note that environment variables are generally in all caps by convention, to visually distinguish them from regular shell variables.

Lists are assigned using the bash-like syntax of ‘:’ delimited elements, rather than with ‘()’ and space delimited elements as ‘set’ uses. When a list is added to, as with the $PATH example, the variable should be within ‘{}’, so that the ‘:’ does not look like a modifier (i.e. using ${PATH} rather than just $PATH).

Examples:

setenv MY_ENV_VAR "some value"setenv PATH ${PATH}:$HOME/abinsetenv DYLD_FALLBACK_LIBRARY_PATH $HOME/abin

Examples of similar commands using bash:

name="Maria Buttersworth"export nameexport name="Maria Buttersworth"export DYLD_FALLBACK_LIBRARY_PATH=$HOME/abin

For more help, see man tcsh.

1.1.8. unset¶

delete a shell variable

This does not just clear the variable, but makes it “not exist”.

Examples:

set value = 7echo $valueunset valueecho $value

The result of the last echo $value command would produce an error,since that variable no longer exists.

1.1.9. unsetenv¶

delete an environment variable

This does not just clear the variable, but makes it “not exist”.

Examples:

unsetenv DYLD_FALLBACK_LIBRARY_PATHunsetenv AFNI_NIFTI_DEBUG

1.2.1. cat¶

display file contents in terminal window

The cat command, short for catenate, is meant to dump all files on the command line to the terminal window.

Examples:

cat AFNI_data6/FT_analysis/s01.ap.simplecat here are four filescat here are four files | wc -l

1.2.2. gedit¶

a text editor for the GNOME Desktop

The gedit program is a graphical text editor that works well across many Unix-like platforms. If you are not sure which editor to use, gedit is a good option. It often needs to be explicitely installed.

Examples:

geditgedit my_script.txtgedit output.proc.subjFT.txt

1.2.3. less¶

a text file viewer

rcr - add this

1.2.4. ls¶

list directory contents

The ‘ls’ command lists the contents of either the current directory or the directories listed on the command line. For files listed on the command line, it just lists them.

Multiple directories may be listed, in which case each directory is shows one by one.

Examples:

lsls $HOMEls AFNI_data6/afnils AFNI_data6/afni AFNI_data6/FT_analysis/FT ~ls -alls -ltrls -ltr ~ls -lSr dir.with.big.files

See Also

Logs Preview - en

Common options:

-a : list all files/directories, including those starting with '.'-l : use the long format, which includes: type, permissions, ownership, size, date (may vary per OS)-t : sort by time (modification time)-r : reverse sort order-S : sort by size of file (e.g. 'ls -lSr')

1.2.5. pwd¶

display the Present Working Directory

The pwd command just shows the present working directory.

Examples:

pwd

1.2.6. tcsh¶

t-shell

This shell (user command-line interface) is an expanded c-shell, with syntax akin to the C programming language. One can start a new tcsh shell by running this command, or one can tell the shell to interpret a script.

Examples:

tcshtcsh my.script.txttcsh -xef proc.subj1234 |& tee output.proc.subj1234

See also

• man tcsh
• man bash
• a Unix book

1.3.1. &¶

run some command in the background

Putting a trailing & after a command will have it run in the background, akin to omitting it and typing ctrl-z followed by bg.

Examples:

suma -spec subj_lh.spec -sv SurfVol+orig &tcsh run.my.script &

Some other uses for & include conditional (&&) and bitwise ANDs (&), as well as piping (|&) and redirection (>&) of stderr (standard error).

1.3.2. \¶

line continuation (or escaping)

Putting a trailing \ at the end of a command line tells the shell that thecommand continues on the next line. This could continue for many lines.

Examples:

echo this is all one long \ command, extending over \ three lines

Note that the latter two lines were indented only to clarify thatecho was the actual command name, while the other textitems were just parameters.

Another use is to tell the shell not to interpret a special character oran alias.

More examples:

ls $HOMEls \$HOMEecho *echo \*ls\ls

Some programs allow for a similar interpretation (and other interpretations).

1.3.3. #¶

pound/hash character: apply as comment or return list length

The pound character has 2 main uses in a t-shell script, to start a commentor to return the length of an array.

In a shell script, if # is not hidden from the shell (in quotes orescaped with \), then from that character onward is ignored by theshell, as if it were not there. The point of this is to allow one toadd comments to a script: text that merely tells a reader what the scriptis intending to do.

For example, if a t-shell script had these lines:

set greeting = pineapple# check whether user wants to say "hi" or "hello"if ( $greeting == hi ) then # the short greeting echo hi thereelse echo hello there # this is a strange place for a commentendif

Then the “check whether user wants” line does not affect the script,nor does the comment “this is a strange place for a comment”.

The output is simply, “hello there”.

Note

Pound characters entered at the command line are not treated as comments,they are treated as any other simple text (possibly because the shellauthors did not see any reason why one might want comments at the commandline, such as for when cutting and pasting scripts).

Another use of # is to get the length of a shell array variable, suchas $path. For example:

 echo my path has $#path directories in it echo the full list is: $path.. note:: this use does not apply to environment variables, such as $PATH

1.3.4. '¶

single quotes

Enclosing text in single quotes tells the shell not to interpret (most of) the enclosed special characters. This is particularly important for cases where special characters need to be passed to a given program, rather than being interpreted by the shell.

With respect to scripting, the most important difference between single and double quotes is for enclosed $ characters, such as with $HOME, $3 or something like $value. Such variable expansions would occur within double quotes, but not within single quotes.

Note

back quotes ` are very different from single ' or double " quotes

Examples:

3dcalc -a r+orig'[2]' -expr 'atanh(a)' -prefix zawk '{print $3}' some.file.txtecho 'my home directory is $HOME'

The first example uses 3dcalc to convert a volume of r-value (correlationvalues) via the inverse hyperbolic tangent function (a.k.a. Fisher’sz-transformation). The first set of quotes around [2] hide the []characters from the shell passing them on to 3dcalc. Then the 3dcalcprogram knows to read in only volume #2, ignoring volumes 0, 1 andanything after 2.

If the [] characters were not protected by the quotes, it would likelylead to a “No match” error from the shell, since the square brackets areused for wildcard file matching.

Alternatively, the quotes could alter go around the entire r+orig[2].

The quotes around atanh(a) are to hide the () characters, again sothat 3dcalc sees that entire expression.

The second example hides both the {} and $ characters. Note that$ is most commonly used to access variable values, such as in $HOME.

The third example just clarifies that shell variables are not expanded,since the output shows $HOME and not /home/rickr, for example.

1.3.5. "¶

double quotes

Enclosing text in double quotes tells the shell not to interpret some of the enclosed special characters, but not as many as with single quotes. This is particularly important for cases where special characters need to be passed to a given program, rather than being interpreted by the shell.

With respect to scripting, the most important difference between single and double quotes is for enclosed $ characters, such as with $HOME, $3 or something like $value. Such variable expansions would occur within double quotes, but not within single quotes.

Note

back quotes ` are very different from single ' or double " quotes

Examples:

3dcalc -a r+orig"[$index]" -expr "atanh(a)" -prefix zecho "my home directory is $HOME"

These examples just demonstrate use of variables within double quotes.The first one uses $index as a sub-brick selector with AFNI’s 3dcalcprogram. In this case, $index might expand to 2, as in the exampleusing single quotes.

The second example (with $HOME) is similar to the one with singlequotes. But the double quote output shows $HOME expanded to the homedirectory (e.g. /home/rickr), while the single quotes output does not(it still shows $HOME).

1.3.6. `¶

back quotes

Back quotes are very different from single or double quotes. While single anddouble quotes are commonly used for hiding special characters from the shell,back quotes are used for command expansion.

When putting back quotes around some text, the shell replaces the quoted textwith the output of running the enclosed command. Examples will make it moreclear.

Examples:

echo my afni program is here: `which afni`count -digits 2 1 6set runs = "`count -digits 2 1 6`"echo there are $#runs runs, indexed as: $runsset runs = ( `count -digits 2 1 6` )echo there are $#runs runs, indexed as: $runs

The first example runs the command which afni, and puts the resultback into the echo command. Assuming afni is at /home/rickr/abin/afni,the first command is as if one typed the command:

echo my afni program is here: /home/rickr/abin/afni

The second example line (count -digits 2 1 6) simply shows the outputfrom the AFNI count program, zero-padded 2 digit numbers from 1 to 6.

The third line captures that output into a variable. Going off on a smalltangent, that output is stored as a single value (because of the doublequotes).

The fourth line displays that output in the terminal window. In this case,the $runs variable has only 1 (string) value, with spaces between the 6run numbers.

The fifth line (again with set runs) sets the $run variable usingparentheses, storing the output as a list (an array) of 6 values).

The final echo line shows the same output as the previous echo line,except that now it shows that there are indeed 6 runs.

1.3.7. ctrl-c¶

terminate a running process (in the current terminal window)

The ctrl-c (while holding the control key down, press c) keystroke is used to terminate the foreground process in the current shell (by sending it a SIGINT signal). It is similar to ctrl-z, but rather than suspending a process, ctrl-c terminates it.

This might be useful when running a shell script that would take a while to complete. Maybe you decide to make a change, or error messages start coming out. If that script is running in the foreground, entering ctrl-c should terminate it.

Example:

1. run 'ccalc' (the prompt is now waiting for an input expression to evaluate)2. type 3+5 and hit <Enter> (it should show the result: Z = 8)3. terminate the program with ctrl-c (the prompt should now be back)

1.3.8. ctrl-z¶

suspend a running process

The ctrl-z (while holding the control key down, press z) keystroke is used to suspend the foreground process in the current shell. The process still exists, but will not run while in the suspended state.

This keystroke is often followed by bg (background: a built-in shell command), to put the newly suspended process in the background. Alternatively, it could be followed by fg (foreground: a build-in shell command), to put the suspended process back in the foreground, as it was in the first place.

Example:

ccalc3+5 - should show the result Z = 8ctrl-z - process 'Suspended', prompt should be backls - works, can type other commandsjobs - shows that 'ccalc' is still suspendedfg - put 'ccalc' back in the foreground3-4 - should show the result Z = -1quit - quit ccalc program

todo:

rcr - consider adding any of these over time...*, ?, [], !, |, :, ~, %, (, {, <, >