See this page as a slide show
CHAPTER 2: Scripting and the Shell
Linux Scripting
- Linux Commands
- Linux Shells: sh, csh, bash
- Shell Features: Redirection and Pipes, History and Editing, Filters
- Shell Scripting
- Variables and Quoting
- Arguments and Functions
- Control Flow
- Arrays and Arithmetic
- Regular Expressions
Linux Commands
- Terse abbreviations!
- <command> <options> <arguments>
- man <command>
Directory Navigation
- Path syntax: /<directory>/<subdirectory>/<file>
- cd <path> - change current directory
- ls <path> - list current (specified) directory
- pwd – show current directory
- mkdir <directory> – create a new directory
- rmdir <directory> – remove a (empty) directory
File Related
- cat, less, more <file> – display file contents
- vi, emacs, gedit <file> - edit file contents
- cp <path> <path> - copy file or directory
- mv <path> <path> - move (rename) file or directory
- rm <path> - remove file or directory
- diff <path> <path> - compare file or directory
Protection Related
- chmod <permissions> <path> - change permissions
- chown <owner> <path> - change (user) ownership
- chgrp <group> <path> - change (group) ownership
Process Related
- ps – display running processes
- kill – terminate running processes
- bg, fg, nice – process control commands
System Related
- shutdown <time> – system shutdown
- reboot – system reboot
- date – system date and time
- time <command> – measures command timing
- whereis <command> – find command instances
- dmesg – system boot messages
Linux Shells
- What is a shell?
- Command-Line Interpreter
- Operating System Interface
- Primitive Language!
- Bourne Shell – sh
- Bourne (1977): Pipeline, Redirection, Variables, Wildcards
- C Shell – csh
- Joy (1978): History, Editing, Aliases, Stacks, Tilde Notation
- Bash Shell - bash
- Fox (1989): Currently used for Unix, Linux, and Mac
Redirection
- Streams: stdin, stdout, and stderr
- Can be redirected to terminal, file, other programs
- Use > for stdout, >> for stderr, < for stdin
- Example: echo "Test Message" > ~/file.txt
- Example: mail –s "Test Mail" johndoe < ~/file.txt
Pipes
- Connect stdout to stdin
- Example: ls | less
- xargs <command> – uses stdin as arguments to command
- Example: find . -name temp.dat | xargs rm
Shell Features
- Editor Selection: set –o vi or set –o emacs
- History – navigates command history
- history – retrieves history buffer
- CTRL-P (up arrow) / CTRL-N (down arrow) moves in command history
- CTRL-R <string> searches history buffer
- Editing - modifies restored commands
- CTRL-B (left arrow)/CTRL-F (right arrow) moves cursor left/right
- Backspace and Delete remove characters
Filter Commands
- Read stdin and write stdout
- sort – sort input line to output lines
- -b : ignore white space
- -f : case insenstive sorting
- -n : compare fields as numbers
- -r : reverse sort order
- -k : specify sorting column
- uniq – print unique lines (cull duplicates)
- tee – copy input to two places
- head, tail – print beginning or head of file
- grep "pattern" – search for text
Shell Scripting
Shell scripts are programs that:
- Allow automation of complex tasks
- Provide batch execution capability
- Used to control periodic processes
- No limit to complexity of scripts
- Have variables and control flow
- Can accept command line arguments
- Can read input and write output and files
- Specific syntax that follows is for bash
Input and Output
- echo "<string>" – send string to stdout
- read <variable> - read variable from stdin
Variables and Quoting
- Variable names are unmarked in assignments
- Example: pathname="/usr/lib"
- Variable names are prefixed with $
- Example: echo $pathname
Arguments
- Scripts accept command-line arguments, just like programs:
- Example: $# equals argc-1, $0 equals argv[0], etc.
Script Syntax
- Initial line of file identifies which shell
- Example: #! /bin/bash
- Comments start with hash mark
- Example: # Make sure to remove all gophers here
- Functions
- Allow grouping of commands
- Can accept parameters
- Can create local variables
- Example: usage() { echo "Usage: $0 <param>"; }
if/then/else
# Spaces count!
if [[ $num -eq 1 ]]
then
echo "Number is one"
elif [[ $num -eq 2 ]]
then
echo "Number is two"
else
echo "Number is $num"
fi
Loops
for datafile in *.zot
do
echo Now processing $datafile
done
for ((i=0; i<$max; i++))
do
echo $i
done
Arithmetic
Variables are strings, force numeric evaluation with $((…))
or let a=2+2
% alpha=1
% beta=2 # no spaces around =
% gamma=$alpha+$beta
% let delta=alpha+beta
% echo $gamma
1+2
% echo $delta
3
Arrays
Somewhat limited capabilities compared to C:
% array=(one two three)
% echo ${array[1]}
two
% echo ${array[*]}
one two three
% echo ${#array[*]}
3
Regular Expressions
- Capabilities beyond many programming languages
- Support pattern matching in grep and vi commands
- Special characters that appear in regular expressions
- . – matches any character
- [chars] – matches any character from given set
- [^chars] – matches any character not in given set
- ^,$ - matches the beginning & end of a line
- \d is [0-9], \w is [A-Za-z0-9_], \s is [ \f\t\n\r]
Script Example
#!/bin/bash
# RunDiscrete - Script to optimize and run SAXS discrete scattering
START=16384; STOP=8388608
date > $1
# Run original code
time ./Discrete Data/1xib.pdb Data/1xib.int >>& $1
for ((size=START; size<=STOP; size*=2))
do
# Create optimized code
./Mesa Discrete.cpp DiscreteMesa.cpp $size >> $1
make # Compile optimized code
# Run optimized code
time (DiscreteMesa Data/1xib.pdb Data/1xib.int) >>& $1
done
Resources
