C2110 UNIX and programming 6th lesson -1C2110
UNIX and programming
Petr Kulhánek, Jakub Štěpán
kulhanek@chemi.muni.cz
National Centre for Biomolecular Research, Faculty of Science
Masaryk University, Kotlářská 2, CZ-61137 Brno
CZ.1.07/2.2.00/15.0233
6th Lesson
C2110 UNIX and programming 6th lesson -2-
Contents
 Scripts
• Scripts vs. programs
• Program compilation
• Running sample script and program
 Variables
• Setting and removing variables
• Variables and processes
• String types
C2110 UNIX and programming 6th lesson -3-
Scripts
 Scripts vs. programs
 Program compilation
 Running sample script and program
C2110 UNIX and programming 6th lesson -4Programs
vs. Scripts
Source code
program
input
output
Compilation
script interpreter
input
output
Program is machine instruction file
processed directly by processor. It is
created by procedure called compilation
from source code.
Compiled languages:
C/C++
Fortran
Script is text file containing commands
and special constructions, these are
processed by interpreter of scripting
language.
Skripting languages:
bash
gnuplot
awk
JavaScript
PHP
C2110 UNIX and programming 6th lesson -5Programs
vs Scripts, ...
No recompilation
Program can generate and
run self running code
Poor optimization
Slower processing
Easy optimization
Fast processing
Recompilation needed
Self run code not available
Source code
program
input
output
Compilation
script interpreter
input
output
C2110 UNIX and programming 6th lesson -6How
to write programs and scripts
Scripts are text files – thus any text editor can be used, that enables saving pure text
(without any format metadata).
Text editors:
 vi
 kwrite
 kate
 gedit
For complex programs and scripts development environments can be used – IDE
(Integrated Development Enviroment). IDE contains next to editor extra tools as: project
manager, debugger and more. Usually for more advanced and complex languages:
JavaScript, Python, PHP, etc.
IDE:
 Kdevelop
 qtcreator
 NetBeans
 Eclipse
C2110 UNIX and programming 6th lesson -7Program
in C
#include <stdio.h>
int main(int argc,char* argv[])
{
printf("This is C program! \n");
return(0);
}
Compilation
$ gcc program.c -o program
Source code
Running program
$ ./program
C language compiler Program name
file program needs permission to execute
C2110 UNIX and programming 6th lesson -8Program
in Fortran
program Hello
write(*,*) 'This is Fortran program!'
end program
$ gfortran program.f90 -o program
$ ./program
Compilation
Source code
Running program
Fortran language compiler Program name
file program needs permission to execute
C2110 UNIX and programming 6th lesson -9Script
in Bash
#!/bin/bash
echo 'This is Bash script!'
Running script
interpret Bash file script.bash does not need permissions to execute
Script
$ bash script.bash
C2110 UNIX and programming 6th lesson -10Script
in gnuplot
#!/usr/bin/gnuplot
set title "This is gnuplot script!"
plot sin(x)
pause -1
interpret gnuplot
Script
$ gnuplot skript.gnuplot
Running script
file script.bash does not need permissions to execute
C2110 UNIX and programming 6th lesson -11-
Exercise
1. Create four directories with names task01, task02, task03, task04
2. From directory /home/kulhanek/Data/programs copy program.c ,
program.f90, skript.bash, a skript.gnuplot to particular directories you
created in 1.
3. Compile source codes of language C and Fortran. Run compiled programs.
4. What is size of compiled program in C language? Open program file in text
editor, what is inside?
5. Run scripts skript.bash a skript.gnuplot.
C2110 UNIX and programming 6th lesson -12Running
scripts
1) Un-direct running
We run interpreter and as its argument we put script name.
$ bash my_bash_script_name
$ gnuplot my_gnuplot_script_name
Scripts does not need permission x (executable).
2) Direct running
We run directly script (shell runs interpreter automatically).
$ ./my_bash_script
$ ./muj_gnuplotu_script
Scripts must have x (executable) set and interpreter (first script line).
C2110 UNIX and programming 6th lesson -13Interpreter
specification
#!/bin/bash
echo “This is bash script!"
#!/usr/bin/gnuplot
set xrange[0:6]
plot sin(x)
pause -1
Script in bash Skript in gnuplot
#!/absolute/path/to/interpreter/of/script
Interpreter specification (first script line):
 If no interpreter is specified, then system shell interpreter is used.
 Interpreter is ignored in case of un-direct running.
C2110 UNIX and programming 6th lesson -14Interpreter
specification
#!/usr/bin/env interpreter
If absolute path may be changed over time (for example by using software modules), it
may be specified dynamically:
Interpreterhas to be in system path of variable
PATH.
#!/usr/bin/env bash
echo “This is bash script!"
#!/usr/bin/env gnuplot
set xrange[0:6]
plot sin(x)
pause -1
Script in bash Script in gnuplot
C2110 UNIX and programming 6th lesson -15-
Exercise
1. Change access permissions to files skript.bash a skript.gnuplot (command
chmod).
2. Make sure that scripts can be run directly.
3. What happens when we use interpreter bash for script skript.gnuplot?
C2110 UNIX and programming 6th lesson -16-
Variables
 Variable setting and unsetting
 Variables and processes
 String types
C2110 UNIX and programming 6th lesson -17-
Variables
In Bash language variable is named memory place, that contain value. Variable value is
always of type string (test).
Variable set:
$ VARIABLE_NAME=value
$ VARIABLE_NAME="value with spaces"
Access to variable value:
$ echo $VARIABLE_NAME
Unsetting of variable:
$ unset VARIABLE_NAME
Overview of all variables:
$ set
No space between variable name and =
C2110 UNIX and programming 6th lesson -18Variables
and processes
Variables
Process: pid, ppid
Process: pid, ppid
Variables
Parent process
child process
Each process has own space for variables
and its values.
Child process when started gets copy of exported variables
and its values from parent process. These variables can be
changed by any way or remove them and new variables can
be defined too. All these changes are not visible to original
variables in parent process and are deleted when child
process finishes.
Export proměnné:
$ export VARIABLE_NAME
$ export VARIABLE_NAME= "value"
export
export with assignment
C2110 UNIX and programming 6th lesson -19-
Strings
In Bash llanguage there are four string types:
• no quotes
A=pokus
B=*
C=$A
• with quotes
A="pokus hokus"
B="* $A"
• single quote (apostrophe)
A='pokus hokus'
B='* $A'
• backward single quote (backward apostrophe)
A=`ls –d`
B=“number : `ls | wc –l`"
Expands to list of files and directories in current
working directory (advanced constructions can be
used)
Value of variable A is inserted
Value of A is inserted but no expansion is done (star
is in quotes)
Text is saved in exact way, no variable insertion, no
expansion is done.
Variable contains value with 2 words separated by space
To place where are backward
apostrophes, command output is
inserted
C2110 UNIX and programming 6th lesson -20Variables
and special symbols
Text expansion order:
Input text (string)
Variable expansion
intermediate
Special characters
expansion (wildcards)
result
Expansion is not done,
if text is in double
apostrophes ""
Expansion is not done,
if text is in single
apostrophes ''
C2110 UNIX and programming 6th lesson -21Commands
for exercise
more prints text from file or standard input by pages (appropriate to view long
texts)
less similar to more with extended functionality (for example movement to both
directions in text)
xargs runs command with arguments that are from standard input. Appropriate to
create long argument list.
grep prints lines from files or standard input that match given search PATTERN
Examples:
$ set | more
lists existing variables and functions by pages
$ cat *.txt | less
prints contents of all files with extension .txt by pages
$ cat directory_list.txt | xargs mkdir
creates directories with names according to contents of file
directory_list.txt
$ grep AHOJ file.txt
prints particular lines from soubor.txt, that contain text AHOJ
C2110 UNIX and programming 6th lesson -22-
Exercise
1. Set variable A to value 55.
2. Print value of variable A (command echo)
3. List all variables. Is there variable A (try to use command less and more)?
4. Use command grep and print line containing variable A record. Select
search pattern independent on variable value.
5. Print all variables with name beginning with A (grep ^TEXT).
6. Change variable A value to "this is long string".
7. Print value of variable A.
8. Unset variable A.
9. Make sure it is unset (use procedure as in 4).
10. Set variables A, B and C as on previous page 19. Check their values by set
or echo.
11. Create file directories.txt, with words pokus1, pokus2, pokus3 on
separate lines. Use command xargs to create directories of same names.