UNIX for beginners

1. Introduction: What is UNIX ?

UNIX is the name of a collection of software known as an operating system (OS) that runs on
most computers. The OS software is the means by which the user communicates with the
computer's central processing unit (CPU) and memory by means of a keyboard and mouse (for
input) and display monitor (for output), in order to perform computations. The OS software is
also responsible for communications between the CPU/memory and the computer's other
peripherals such as disks, tapes, printers, dials, networks, etc., allowing these to be shared with
other users (multi-user system), and/or with other jobs that a single user is running
simultaneously (multi-tasking system). The OS ensures that no two users or jobs can access the
same device (CPU, memory, peripherals) at the same time; one is allowed to proceed while the
other is forced to wait until the device is no longer busy.

The user should realise that the name UNIX does NOT refer to a single well-defined collection
of software (even though the name was originally meant to imply "unique system"!), and that
there is no such thing as "standard UNIX". UNIX is rather a generic term for a number of
superficially similar collections of software that differ in their detailed modes of operation,
depending on the supplier of the OS software (usually but not always the same supplier of the
CPU). These apparently arbitrary variations are a major source of confusion and frustration
particularly for novice users.

2. Basic concepts.
2.1. The UNIX nut: kernel and shell.

The main control program in a UNIX OS is called the kernel. However the kernel does not
allow the user to give it commands directly; instead when the user types commands on the
keyboard they are read by another program in the OS called a shell which parses, checks,
translates and massages them in various ways to be described later, then passes them to the
kernel for execution. (The analogy is with a nut - as in walnut - the important part of which is
the kernel inside; the shell is merely the face that the nut presents to the outside world!) Modern
shells aim to reduce the amount the user has to type by providing facilities such as command
recall and edit, command spelling correction, command or filename completion, and "wildcard"
characters (characters in filenames that represent multiple possibilities).

There are a number of different shells available, with names such as sh, csh, tcsh, ksh, bash, each
with different rules of syntax; these are partly though not completely responsible for the diversity
of UNIX. Once the command has been interpreted and executed, the kernel sends its reply,
which may simply be a prompt for the next command to be entered, either directly to the display
monitor, or more usually if a windowing system (e.g. X-windows) is in operation, via a display
manager (e.g. xdm). This is a program responsible for deciding where and in what form the
output will appear on the display monitor. If for any reason the kernel cannot perform the
command requested (wrong syntax, for example), the reply will be an error message; the user
must then re-enter the corrected command.

2.2. Commands and processes.

The kernel and the shell programs running in the CPU are examples of processes; these are self-
contained programs that may take over complete control of the CPU. Although there can only be
one kernel process running in a particular CPU, there may be any number of shell and other
processes, subject of course to memory limitations.

Some commands to the shell are internal (or built-in), that is they only involve the shell and the
kernel. Others are external and may be supplied with the OS, or may be user-written. An
external command is the name of a file which contains either a single executable program or a
script. The latter is a text file, the first line of which contains the name of a file containing an
executable program, usually but not necessarily a shell, followed by a sequence of commands for
that program. A script may also invoke other scripts - including itself! Its purpose is simply to
avoid having to re-type all the command it contains.

A command may also be an alias for an internal or external command (e.g. the user may not like
the UNIX name "rm" for the command which deletes files, and may prefer to alias it to "delete").

The external command may optionally cause execution of the shell process to be temporarily
suspended, and then run another program, which may then take over input from the keyboard
and mouse and send output for display. The shell may or may not wait for the program to finish,
before it wakes up again and cause its prompt to be displayed. It is very important that the user
be continuously aware of which process is currently reading keyboard input: the shell or another
program, because they usually speak completely different languages!

The above is an example of a parent process - the shell, and a child process - the external
program. In fact the child could just as well have been, and often is, another invocation of the
same shell, or of a different shell, and the child process can be the parent of other child and so on
(almost) ad infinitum. Consequently a typical UNIX system has many processes either waiting
or running.

2.3. UNIX plumbing: pipes and inter-process communication.

Many UNIX commands by themselves perform very simple tasks; the power of UNIX derives
from its capability to combine these in order to perform more complex tasks. Commands may be
run sequentially so that the output which results when each command acts on its input data
becomes the input for the next command in the sequence - this is called a pipe. Shell scripts may
also make use of pipes and other control structures such as variables, condition tests and loops.
UNIX also has extensive facilities for inter-process communication (in addition to the pipe
mechanism).

2.4. Foreground, background and batch.

The user needs to be aware that there are 2 basic ways of running jobs (i.e. commands, programs
and scripts) on a UNIX system: foreground and background. There is also batch mode, but
this is similar to background, with the exception that the jobs are held in a batch queue for
sequential execution instead of all being run simultaneously. In foreground mode the parent
process is suspended while the child process runs, taking over the keyboard and monitor; when
the child process terminates the parent process resumes from where it was suspended.

In background mode the parent process continues to run using the keyboard and monitor as
before, while the child process runs asynchronously. In this case it is advisable that the child
process get all its input and send all its output to or from files and not to or from the keyboard
and monitor, in order to avoid confusion with the parent process's input and output. When the
child process terminates, either normally or by user intervention, the event has no effect on the
parent process, though the user is informed by a message sent to the display. The user may also
elect to place a child process already running in foreground into the background and resume the
parent process, or to bring a background process into the foreground. The user may actively
terminate (kill) any process, provided he/she owns it (the user owns any process he/she initiates
plus all descendants of that process), or downgrade (but not upgrade!) the priority of any owned
process.

2.5. UNIX file system.

Like other OS's UNIX organises information into files, and related files may be conveniently
organised in directories. Files may contain text, data, executable programs, scripts (which are
actually just data for a scripting program such as a shell), and may also be links to other files, or
to physical devices or communications channels.

The directory structure is hierarchical with the root directory, indicated by a forward slash (/), at
the base of the tree. This may contain files as well as other directories such as /bin, /etc, /lib,
/tmp, /usr, and /d. Actually in this example the root directory will contain directory files called
bin, etc, lib, tmp, usr and d, each of which contains a list of files and their locations on the disk
for each of the corresponding directories. Each directory may contain further ordinary files and
directory files, and so on. The / character is used to delimit the components of the name. For
example the /d directory may contain directories such as /d/user1 and /d/user2 and these may
contain the users' home directories such as /d/user1/tom, /d/user1/dick and /d/user2/harry, which
are the directories that users tom, dick and harry respectively normally see when they first login
to the system.

The entire directory hierarchy may reside on a single physical disk, or it may be spread across
several disks; the boundaries between physical disks cannot be seen merely by looking at the
directory hierarchy. Your system administrator will decide where your home directory is to be
both physically and logically located.

Every file in the hierarchy is identified by a pathname, this is merely a description of the the
path you have to traverse to get from the root directory to the file. E.g. the file junk.data (not a
wise choice for a file containing data you wish to keep!) in directory /d/user1/tom/keep has the
pathname /d/user1/tom/keep/junk.data . This is an absolute pathname, because it starts with a / .
The pathname of a directory may be optionally terminated by a / ; e.g. in the example above
/d/user1/ means the same as /d/user1 . Strictly, a filename is distinct from a pathname; a
filename is just one of the components of the pathname delimited by /'s.

Relative pathnames which have a start point anywhere but / in the hierarchy may be used
instead, and are often more convenient. Starting from /d/user1/tom/keep the relative pathname
of the previous example is just junk.data or ./junk.data (because "." means the current directory).
Starting from user tom's home directory it would be keep/junk.data. User dick in his home
directory might refer to the same file either by its absolute pathname or by the name
../tom/keep/junk.data (".." means the parent directory which contains the current directory). User
harry residing in /d/user2/harry would have to use the absolute pathname or
../../user1/tom/keep/junk.data .

A useful shorthand for the home directory is ~ (though this syntax is not supported by all shells),
so Tom can also refer to the same file by the absolute pathname ~/keep/junk.data, and Harry can
use ~tom/keep/junk.data .

Another shorthand is the use of "wildcard" characters in filenames, technically called filename
globbing. The * character in a filename represents any string of characters, including no
characters; the ? character represents any single character; a string of characters between []
represents any one of those specific characters. These wildcard characters may be used more
than once, and may appear in combination in a pathname. Thus * by itself would be expanded to
a complete list of filenames in the current directory, whereas ? would be expanded only to a list
of 1 character filenames (if any), ?? to a list of 2 character filenames, and so on. If there are files
called "fee", "fie", "foe" and "fum" in the current directory, the strings f* and f?? would be
expanded to the full list of names, whereas f?e and "f[eio]e" would be expanded to "fee fie foe"
("fum" doesn't match the last two patterns). It is important to understand that it is the shell that is
responsible for this wildcard expansion, and it does it completely mechanically without regard
for any "intended" meaning (see example of the mv in Unix exercises section).

Last, but not least, note that UNIX is always fussy about the case of letters in commands,
usernames, passwords and filenames; so Junk.data is not the same file as junk.data .

2.6. The shell environment.

Each instance of the shell has its own environment of aliases, local variables and global (or
environment) variables. Aliases and local variables are local to the shell, and are not passed on
to any other process, whether parent or child. Global variables are inherited from the parent by
the child, but not vice versa. Local variables are conventionally given lower case names, while
global variables have upper case names. Global variables include the home directory (HOME),
the path (PATH), the current directory (PWD), the shell (SHELL), and the terminal type
(TERM).

The path is a list of directory filenames which is searched for external commands or scripts
whenever the command or script name does not contain a directory specification; if there is more
than one instance of the file in the path, the first one found is executed. Note that the alias list is
always searched first, followed by the list of built-in commands, followed by the directories in
the path in sequence. If the command contains a directory specification (e.g. ./run) none of the
alias, built-in command or path lists are checked.

2.7. Syntax of UNIX commands.

The general form of a UNIX command is: command [option(s)] [argument(s)] (the [] here
indicate that the items they contain are optional; they are not part of the syntax).

If a typing error is made the line may be changed using the left/right arrow keys to move the
cursor and the Backspace key to delete the character to the left of the cursor; new characters are
inserted before the cursor. When the line is correct use the Enter key to execute the command.
It is not necessary to move the cursor to the end of the line before pressing Enter. The command
may be cancelled before execution by using Ctrl-u (hold down the Ctrl key and press the u key).
If an incorrectly spelled command is entered and spelling correction is enabled in the shell, the
shell will attempt to correct the mistake and ask for verification.

If the shell has filename completion enabled, use of the Tab key after part of a command or
filename has been typed will cause the shell to attempt completion of the name, up to the
character where the result is unique. Use of the Ctrl-d key will cause all names that match what
has been typed to be listed.

The options and arguments if present must be separated from the preceding item by a least 1
space. However multiple options may or may not need to be separated from each other by at
least 1 space; multiple arguments are always separated from each other by at least 1 space.
Options usually start with -, but occasionally it is a +, and sometimes the - or + may be omitted.

A line may contain several commands (each possibly followed by options and/or arguments)
separated by semicolons (;). The commands are executed in sequence, just as if they had been
typed on separate lines. If it is necessary to continue a command onto the next line, end the line
with a backslash (\), press Enter and continue typing on the next line.

In a script anything after a # on a line is treated as a comment, i.e. it is ignored.

To background a command simply add an ampersand (&) on the end.

Commands may be piped using a vertical bar (|) to separate them. As an alternative to piping the
output may be redirected to write to a file using >filename or appended to the file using
>>filename. This only redirects the standard output stream; redirection of error messages
(standard error stream) requires a different syntax which is shell-dependent. The standard
input stream may be redirected to read from a file using <filename. Either or both standard
input and output may be redirected. In a script the standard input stream may be redirected to
read from the script by using <<terminator, e.g.:
command [option(s)] [argument(s)] <<EOD
Input data goes here.
EOD
The terminator above must match the one given on the command line exactly and must start in
the first character position. Any sequence of characters may be used in the terminator, except for
special characters like &|<>'"\ . If it is preceded by a backslash (\) this has a special meaning:
variables beginning with $ in the input data are not treated as shell variables.

2.8. Getting help.

Knowing how to get information from the computer is always a first priority! The most common
method is by means of the "manual pages", by typing man command where command is what
you want information on. Unfortunately this doesn't help if you don't know what you are looking
for, and UNIX's command names are far from obvious! You can try typing man -k word .
This searches the headings of all the manual pages for word, and may produce both useless and
useful information on what to try next! Some systems have info installed; this is much better
organised than man, though it may not be complete. Type info followed by h if you're a first-
time user, then follow the instructions. Typing help on some systems gives you information on
the built-in shell commands; alternatively try man csh (or whatever shell you're using).

3. UNIX commands.
3.1. Process and screen control.

Note that some of the Ctrl key functions may have been altered by an stty command; use stty -a
to get the current settings.

Key Function
Ctrl-c Kill foreground process
Ctrl-z Suspend foreground process
Ctrl-d Terminate input, or exit shell
Ctrl-s Suspend output
 Ctrl-q Resume output
Ctrl-o Discard output
Ctrl-l Clear screen

3.2. Line recall and editing (T shell).

Key or command Function

Up-arrow Recall previous command
Down-arrow Recall next command
!n Recall history line n
!text Recall last line beginning with text
Left-arrow Move cursor left
Right-arrow Move cursor right
Ctrl-a Move cursor to beginning of line
Ctrl-e Move cursor to end of line
Backspace or Delete Delete character to left of cursor
Ctrl-d Delete character under cursor
Ctrl-u Delete whole line
Ctrl-k Delete line from cursor on
Ctrl-w Delete line to left of cursor
Ctrl-y Paste deleted text
Ctrl-t Transpose characters
Ctrl-r Refresh line

3.3. Filename completion.

Key Function
 Tab Complete filename up to next non-unique character
Ctrl-d List filenames matching partial name

Note that Ctrl-d has 4 possible functions, depending on the context.

3.4. Input/output redirection and piping (C/T shell).

Operator Function
< Redirect standard input from file
<< Redirect standard input from command source
> Redirect standard output to file
>! Redirect standard output and overwrite file
>> Redirect standard output and append to file
>>! Redirect standard output to file or append to file
>& Redirect standard output/error to file
>>& Redirect standard output/error and append to file
>>&! Redirect standard output/error to file or append to file
| Pipe standard output to standard input
|& Pipe standard output/error to standard input
`command` Replace command with its output

3.5. Table of equivalent commands for DOS users.

This table and the next should be used in conjunction with the DOS "help" and UNIX "man"
commands on the particular operating system in use to check the definitive specification of the
command options and arguments, as these often vary between different implementations of the
OS. Note that {} indicates a required variable argument; [] indicates an optional one.

DOS command Unix command Function

help [] man [] {} Provide information about command
chkdsk [] df [] Show disk space
dir/w [] ls [] Wide directory listing
dir [] ll [] Long directory listing
dir/o:-d [] ll -t [] Ditto in reverse creation order
dir/s [] ll -R [] Recursive long listing
dir/p/s [] ll -R [] | more Ditto with pausing
cd pwd Show current directory
cd {} cd {} Change directory
cd .. cd .. Change to parent directory
cd \ cd Change to home directory
md {} mkdir {} Create empty directory
rd {} rmdir {} Delete empty directory
type {} cat [] [] List file(s)
type {} | more more {} [] Ditto with pausing
tv {} less {} [] Ditto
copy {} {} cp {} {} Copy file
rename {} {} mv {} {} Rename file
move {} {} mv {} {} Move file
sort {} sort {} Sort file
edit {} emacs {}& Edit file
del {} rm {} [] Delete file(s)
del/p {} rm -i {} [] Ditto with confirmation
deltree {} rm -r {} Recursive delete directory
pkzip {} gzip {} Compress file(s)
pkunzip {} gunzip {} Decompress file(s)
msbackup [] tar cv . Make backup
msbackup [] tar xv Restore from backup
attrib {} {} chmod {} {} Change file attribute(s)
 fc {} {} diff {} {} List file differences
find "{}" {} grep {} {} Search file(s) for character(s)
print {} lpr -P{} [] Print file
print lpq -P{} List printer queue
print/c lprm -P{} {} Delete print job
doskey/h history Show command history
doskey {}={} alias {} {} Create command alias
set set Show local variables
set {}={} set {}={} Set local variable
path echo $PATH Show executable path
path {} setenv PATH {} Set executable path
for {} {} foreach {} {} Loop command
command tcsh [] Start child shell
{} [] {} [] Run program or script
rem [] # [] Use comment in script
echo {} echo {} Display message in script
if {} {} if {} {} Conditional command
goto {} goto {} Jump to label in script
cls Ctrl-l Clear screen
Ctrl-c Ctrl-c Kill foreground process
Ctrl-z Ctrl-d Signal end of input
Pause Ctrl-s Suspend output to screen
Space Ctrl-q Resume output to screen
exit exit [] Exit from script or shell

3.6. Additional useful UNIX commands by category.

3.6.1. File manipulation.

 Unix command Function
du [] Show disk usage
ln {} {} Create directory entry (hard link)
ln -s {} {} Create soft link to file
file {} Show type of file
which {} Locate executable file in path
touch {} Create empty file or change file access time
tee {} Copy standard input to file and standard output
wc {} Show file length
head [] List top lines of file
tail [] List bottom lines of file
fgrep {} [] Search file(s) for fixed string
egrep {} [] Search file(s) for extended regular expression
find {} [] Multiple file commands
cut [] Extract columns from file
sed {} [] Edit file in stream mode
awk {} [] Process column data
fold [] Fold long lines in file
paste [] Merge lines of files
zcat [] List compressed file
dd {} {} Convert file format
od {} Dump file
nl [] Number lines in file
source {} Read commands from file

3.6.2. Process control.

Unix command Function
yppasswd Change password
stty Show or set terminal characteristics
bindkey Show or set key bindings
alloc Show memory allocation
limit Show process limits
limit {} {} Change process limit
umask {} Change permission for new files
xargs {} [] Execute command with passed arguments
tr {} {} Translate character(s)
setenv Show global variables
setenv {} {} Set global variable
unset {} Unset local variable
unsetenv {} Unset global variable
echo ${} Show value of variable
nice {} [] Run command at low priority
renice {} {} Reduce priority of command
Ctrl-z Suspend foreground process
jobs List background jobs
ps [] Show process status
bg [] Put job in background
fg [] Put job in foreground
stop {} Suspend background process or job
kill {} Signal or kill process or job
batch [] [] Submit command script to batch queue
w List logged-in users
sleep [] Wait for time interval
 time [] Time a command
while {} Conditionally execute loop
logout Terminate current session

3.6.3. Networking.

Unix command Function

finger [] List user information
talk [] Exchange messages with other user
pine Use e-mail
ftp [] Transfer file(s) via network
telnet [] Remote login via network
rlogin [] Ditto
rsh {} [] Remote shell command via network
rcp {} {} Copy file(s) via network

3.6.4. Programming.

Unix command Function

ci {} Check file into revision control
co {} Check file out of revision control
make [] Update program
f77 {} Compile Fortran 77 program
fsplit {} Split Fortran source into subroutines
cc {} Compile C program
c++ {} Compile C++ program
perl {} Compile and run Perl program
3.6.5. Miscellaneous.

Unix command Function

date Show today's date
cal Show calendar
bc Evaluate arithmetic expression(s)

4. Emacs survival guide.

Emacs has a vast range of commands, here is just a brief personal selection of the ones I use
most.

Emacs command Function

Ctrl-h Get online help (e.g. Ctrl-h t for tutorial)

Ctrl-x Ctrl-f Open file in new buffer

Ctrl-x Ctrl-s Save active buffer to existing file
Ctrl-x Ctrl-w Save active buffer to specified file
Ctrl-x s Prompt to save changed buffers to their files
Ctrl-x i Insert another file
Ctrl-x Ctrl-b List all buffers
Ctrl-x b Select specified buffer
Ctrl-x k Kill specified buffer

Note that the above file and buffer manipulation commands are not needed for versions of Emacs
that run in an X-window and have a File/Buffers menu bar. In the following "motion"
commands note that the Alt Gr key sometimes works as Alt.

Emacs command Function

Up/down arrow Move up/down 1 line
Left/right arrow Move left/right 1 character column
Alt-f Move forwards one word
Alt-b Move backwards one word
Ctrl-e Go to end of line
Ctrl-a Go to beginning of line
Alt-> Go to end of file
Alt-< Go to beginning of file
Ctrl-v Go down one screenful
Alt-v Go up one screenful
Ctrl-l Centre current line
Alt-x goto-line
Go to line number n
n

Ctrl-s Incremental search forwards

Ctrl-r Incremental search backwards
Alt-% Global replace with prompt
Ctrl-g Cancel current operation

Delete Delete character before cursor

Ctrl-d Delete character under cursor
Ctrl-k Kill to end of line or delete blank line
Ctrl-y Paste in (yank) last block of text killed or selected
Alt-y Paste in any previous block of text killed or selected
Ctrl-_ Undo last change (may be repeated)
Ctrl-Space Set mark
Alt-w Select region between mark & cursor
Ctrl-w Kill region (cut) between mark & cursor
Note that the above cut and paste commands are not needed for versions of Emacs that run in an
X-window and have an Edit menu. Also the mouse can be used to select text by dragging with
the left button down, moving the mouse cursor to the insertion point and using the middle button
to paste.

Emacs command Function

Ctrl-c Ctrl-r Column numbers (Fortran mode only - starts at 0!)
Ctrl-c Ctrl-w Make window 72 columns wide for Fortran
Ctrl-x 2 Split window vertically
Ctrl-x 3 Split window horizontally
Ctrl-x o Select another window
Ctrl-x ^ Make window taller
Ctrl-x } Make window wider
Ctrl-x 1 Kill all but active window
Ctrl-x 0 Kill active window
Alt-x shell Start shell in Emacs window
Ctrl-x Ctrl-c Exit Emacs

Some of the above functions are not implemented in some versions of Emacs.

5. Some basic vi commands.

Vi command Function
:set nu Show line numbers
:set ic Ignore case differences when searching
:set ai Set automatic indent
:set sm Show matching ( or { with ) or } in insert mode

Up/down arrow Move up/down 1 line

Left/right arrow Move left/right 1 character column
0 $ Go to 1st/last column of current line
Enter Go down to 1st printable character of next line
nw nb Move right/left n words (1 word if n omitted)
nG Go to line n (end of file if n omitted)
Ctrl-f Ctrl-b Page forward/backward 1 screen
Ctrl-d Ctrl-u Page forward/backward half a screen
[[ ]] Go to beginning of current/next C function

/expressionEnter Search forwards for expression

?expressionEnter Search backwards for expression
n N Repeat last / or ? command in same/reverse direction

ytarget Copy (yank) text up to target to buffer

Y Copy current line to buffer

itextEsc Insert text before cursor

otextEsc Open new line below cursor and insert text
r Replace character under cursor with next typed
RtextEsc Replace text

Backspace In insert mode, delete character before cursor

x X Delete character under/before cursor
nx Delete n characters under and to right of cursor
nX Delete n characters before cursor
dd Delete current line
ndd Delete n lines
 D Delete from cursor to end of line

p P Put back yanked or deleted text below/above current line

J Join current and next lines
Global replace (g=every occurrence on line, c=prompt)
:m,n s/old/new/gc
m=. means from current position, n=$ means to EOF
u Undo last change

:q Quit, provided no changes were made

:q! Quit without saving
:w Save (write) changes
:m,n w file Save lines m through n (default=all) to file
:x Save changes and quit

6. Unix exercises.
# <-- Note this means a comment - you don't have to type the comments!
# DON'T FORGET TO USE LINE RECALL AND EDIT - IT WILL SAVE YOU A LOT OF TYPING!

# Set variable P to the PDB data directory.

setenv P /public/pdb/data # Do this once for each instance of the shell.

6.1. emacs exercise.

# First copy a file: note the "." at the end!
cp $P/pdb6lyz.pdb .
# ... and the character after "6" is an ell not a one.
# Set mode to write:
chmod +w pdb6lyz.pdb # Don't forget to use filename completion.
# Define display for X application (once per shell):
setenv DISPLAY lundynn:0
# Edit the file in background; note the ampersand (&):
emacs pdb6lyz.pdb&
# You'll find it easier if you make your shell and Emacs windows wider.

6.2. sed & awk examples.

cp $P/pdb6lyz.pdb . # Make a fresh copy.
sed s/GLU/GLN/ pdb6lyz.pdb # Example of stream editing.
sed s/GLU/GLN/ pdb6lyz.pdb >! new.pdb
diff pdb6lyz.pdb new.pdb # Check that new file is different.

awk '($1=="ATOM") {print $6,$7,$8}' pdb6lyz.pdb

awk '($1=="ATOM") {print $4}' pdb6lyz.pdb
awk '($1=="ATOM") {if ($5!=s) {print $4; s=$5}}' pdb6lyz.pdb >! 6lyz.seq
cat 6lyz.seq

6.3. alias examples.

alias # See what aliases you have.
history
alias h history # Aliases save typing !
h
ls -l
alias ll ls -l # You may have this already.
ll
alias lh 'ls -Alt \!* | head'
lh # Lists 10 most recent files.
lh *.pdb

alias run '(time tcsh \!^:r.csh) >&\! \!^:r.log&'

# Now make a script with emacs, e.g. "job.csh" and type "run job".

6.4. cat & mv examples.

cat >! file1.c
This is file1.c
Ctrl-d # This means hold down the "Ctrl" or "Control" key and
# then press the "d" key.
cat >! file2.c
This is file2.c
Ctrl-d

# In VMS & DOS the following is OK: ren *.c *.cpp

alias mv # mv may be aliased to "mv -i".

unalias mv # Remove "-i" safety check.

cat file1.c
cat file2.c
mv file?.c file?.C # Note Unix distinguishes lower and upper case!
cat file1.C # What happened to your .c files? Explain why!
cat file2.C

6.5. foreach example.

# First, re-create file1.c and file2.c as before.
rm file?.C # Delete the old output files.
foreach x (file?.c)
mv $x $x:r.C
end # Should be OK now!

6.6. Piping and backquoting examples.

setenv Q /public/pdb/current/ps # Saves typing!
grep -h PROTEINASE $Q/*
ll $Q | head -6 # First 5 files in alphanumeric order.
ll -t $Q | head -6 # First 5 files in time-reversed order.
ll -t $Q | tail -5 # Last 5 files in time-reversed order.
grep -h PROTEINASE `ls $Q/* | head -5` # Note ` not ' !
grep -h PROTEINASE `ls -t $Q/* | head -5`
grep -h PROTEINASE `ls -t $Q/* | tail -5`
# What's the purpose of the "-h" flag on the grep command,
# and why is it necessary to specify "$Q/*" ?

6.7. grep & find examples.

ls $P # Works.
ls $P/* # Fails!

grep ASPARTIC $P/*.pdb # Fails!

set echo
grep ASPARTIC $P/pdb1pp?.pdb # Now you see expanded command.
unset echo

find $P -name \*.pdb -exec grep ASPARTIC {} \;

# This is too slow! So just select a few files:
find $P -name pdb1pp\?.pdb -exec grep ASPARTIC {} \;

# No filenames are printed:

# Insert -print before -exec above (use line recall!).
# Now you get all filenames!

find $P -name pdb1pp\?.pdb -print | xargs grep ASPARTIC

# The right way to do it!

6.8. diff examples.

# Create file1 containing: ab
# Create file2 containing: a b
# Create file3 containing: a b

diff file1 file2

diff -ws file1 file2
diff -bs file1 file2
diff file2 file3
diff -bs file2 file3
6.9. bg/fg examples.
stty -tostop # Allows output from background job.
set notify # Allows notification of background job status.
sleep 120; echo wakey wakey&
jobs
fg
Ctrl-z
jobs
bg
jobs
# etc.

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© IJT 06-Oct-1999