BioGem.Org » Information Technology http://www.biogem.org Bioinformatics Blog Site.. Sat, 03 Jul 2010 07:57:38 +0000 http://wordpress.org/?v=2.8.4 en hourly 1 Embedding Perl into Perl http://www.biogem.org/2010/06/embedding-perl-into-perl.html http://www.biogem.org/2010/06/embedding-perl-into-perl.html#comments Sun, 06 Jun 2010 17:39:24 +0000 Ashok Kumar http://www.biogem.org/?p=289 This article describes embedding a Perl script into a Perl script. This program is an Common Gateway Interface, which reads ASCII files through file upload and displays content of the file. The Perl script upload.pl is called through the Perl script file-upload.pl using function eval{ }. This program can be modified to call by reference function, to access in other programs too.

file-upload.html
<html>
<head>
<title>File Upload</title>
</head>
<body>
<form method=”post” action=”/cgi-bin/file-upload.pl” enctype=”multipart/form-data”>
Enter the file to upload:<br>
<input name=”file” size=”45″ type=”file”><br>
<p>
<input name=”reset” type=”reset”>
<input name=”submit” value=”Upload” type=”submit”>
</p>
</form>
</body>
</html>

file-upload.pl
#!/usr/bin/perl
eval { require “upload.pl” };
my @x = upload();
print “Content-type: text/html\n\n”;
print “<font face=’courier new’>”,@x,”</font>”;

upload.pl
#!/usr/bin/perl
use strict ‘refs’;
use lib ‘..’;
use CGI qw(:standard);
use CGI::Carp qw(fatalsToBrowser);
sub upload()
{
my $file = param(’file’);
while (<param(’file’)>)
{
@_ = <$file>;
}
return (@_);
}

Note: Both Perl scripts must granted file permission (0755)

]]> http://www.biogem.org/2010/06/embedding-perl-into-perl.html/feed 1 Running JAVA program in Linux Ubuntu http://www.biogem.org/2009/12/running-java-program-in-linux-ubuntu.html http://www.biogem.org/2009/12/running-java-program-in-linux-ubuntu.html#comments Wed, 16 Dec 2009 15:49:39 +0000 Ashok Kumar http://www.biogem.org/?p=181 Steps to run JAVA program in Ubuntu:

1. Go to Applications > Accessories > Terminal, to open terminal window.

2. Type the following in command line

gedit Add.java

3. Enter the code bellow in the editor.

/* Addition of two numbers – Add.java */
import java.io.*;
class Add
{
public static void main(String args[])
{
InputStreamReader ISR = new InputStreamReader(System.in);
BufferedReader BR = new BufferedReader(ISR);
int a = 0, b = 0;
try
{
System.out.print(”Enter the first number: “);
a = Integer.parseInt(BR.readLine());
System.out.print(”Enter the second number: “);
b = Integer.parseInt(BR.readLine());
}
catch(Exception e)
{
System.out.println(”Check the program.”);
}
System.out.println(”Addition of ” + a + ” + ” + b + ” is” + (a+b));
}
}

4. Save the file and close to return to terminal window.

5. Firstly compile the code using the following command

javac Add.java

That would produce an class file you may need to run the program.

7. Now run this executable using the following command

java Add

8. Output should show as follows

Enter the first number: 49
Enter the second number: 2
Addition of 49 + 2 is 51

Note: If java is not present in the system, download it through terminal window using command sudo apt-get install sun-java6-bin sun-java6-jre sun-java6-jdk

]]> http://www.biogem.org/2009/12/running-java-program-in-linux-ubuntu.html/feed 9 Installing and Configuring XAMPP in Windows 7 http://www.biogem.org/2009/12/installing-and-configuring-xampp-in-windows-7.html http://www.biogem.org/2009/12/installing-and-configuring-xampp-in-windows-7.html#comments Mon, 14 Dec 2009 16:29:30 +0000 Ashok Kumar http://www.biogem.org/?p=148 Many people know from their own experience that it’s not easy to install an Apache web server and it gets harder if you want to add MySQL, PHP and Perl.

XAMPP is an easy to install Apache distribution containing MySQL, PHP and Perl. XAMPP is really very easy to install and to use – just download, extract and start.

At the moment there are four XAMPP distributions:


* XAMPP for Linux

The distribution for Linux systems (tested for SuSE, RedHat, Mandrake and Debian) contains: Apache, MySQL, PHP & PEAR, Perl, ProFTPD, phpMyAdmin, OpenSSL, GD, Freetype2, libjpeg, libpng, gdbm, zlib, expat, Sablotron, libxml, Ming, Webalizer, pdf class, ncurses, mod_perl, FreeTDS, gettext, mcrypt, mhash, eAccelerator, SQLite and IMAP C-Client.

* XAMPP for Windows

The distribution for Windows 2000, 2003, XP and Vista. This version contains: Apache, MySQL, PHP + PEAR, Perl, mod_php, mod_perl, mod_ssl, OpenSSL, phpMyAdmin, Webalizer, Mercury Mail Transport System for Win32 and NetWare Systems v3.32, Ming, JpGraph, FileZilla FTP Server, mcrypt, eAccelerator, SQLite, and WEB-DAV + mod_auth_mysql.

* XAMPP for Mac OS X

The distribution for Mac OS X contains: Apache, MySQL, PHP & PEAR, SQLite, Perl, ProFTPD, phpMyAdmin, OpenSSL, GD, Freetype2, libjpeg, libpng, zlib, Ming, Webalizer, mod_perl.

* XAMPP for Solaris

The distribution for Solaris (developed and tested with Solaris 8, tested with Solaris 9) contains: Apache, MySQL, PHP & PEAR, Perl, ProFTPD, phpMyAdmin, OpenSSL, Freetype2, libjpeg, libpng, zlib, expat, Ming, Webalizer, pdf class. WARNING: This version of XAMPP is still in the first steps of development. Use at you own risk!

Easy installation and deinstallation

To install XAMPP you only need to download and extract XAMPP, that’s all. There are no changes to the Windows registry (not true if you use the Windows installer version of XAMPP) and it’s not necessary to edit any configuration files. It couldn’t be easier!To check that XAMPP is working some sample programs are included, there is a small CD collection program (written in PHP using MySQL) and a small guest book software (written in Perl) and several other demonstration utilities.

If you decide that XAMPP isn’t needed any more just delete the XAMPP directory and it’s completely removed from your system.

However if you use the Windows installer version of XAMPP it’s recommended to use the uninstall feature. As every installer the installer will make registry entries to remember the install.

Steps to install:

Step 1:


Step 2:


Step 3:


Step 4:

XAMPP

Step 5:

XAMPP

Step 6:

XAMPP

Step 7:

XAMPP

Step 8:

XAMPP

Step 9:

XAMPP

Step 10:

XAMPP

Step 11:

XAMPP

Step 12:

XAMPP

Step 13:

XAMPP

Step 14:

XAMPP

After changing to new password, open C:\xampp\phpMyAdmin\config.inc.php in a text editor. Go to line 21 [$cfg['Servers'][$i]['password'] = ”;] and change it to new password [$cfg['Servers'][$i]['password'] = ‘new_password’;].


]]> http://www.biogem.org/2009/12/installing-and-configuring-xampp-in-windows-7.html/feed 19 Two methods to run PHP script http://www.biogem.org/2009/12/two-methods-to-run-php-script.html http://www.biogem.org/2009/12/two-methods-to-run-php-script.html#comments Tue, 08 Dec 2009 16:54:53 +0000 Ashok Kumar http://www.biogem.org/?p=140 HTML with PHP :-
HTML: add.htm
<html>
<head>
<title>Adding two numbers</title>
</head>
<body>
<form action=”add.php” method=”post”>
Enter the first number: <input type=”text” name=”a” size=10><br>
Enter the second number: <input type=”text” name=”b” size=10><br>
<input type=”submit” name=”submit” value=”ADD”>
</form>
</body>
</html>
PHP: add.php
<html>
<head>
<title>Adding two numbers</title>
</head>
<body>
<?php
$a=$_POST["a"];
$b=$_POST["b"];
$c=$a+$b;
print “Addition of $a and $b is $c.”;
?>
</body>
</html>
Only with PHP :-
<?php
$a = $_POST["a"];
$b = $_POST["b"];
if (!isset($_POST['add']))
{  // If page is not submitted to itself echo the form
?>
<html>
<head><title>Adding Two Numbers</title></head>
<body>
<form method=”post” action=”<?php echo $PHP_SELF; ?>”>
Enter the first number: <input type=”text” size=”12″ maxlength=”12″ name=”a”></br>
Enter the second number: <input type=”text” size=”12″ maxlength=”36″ name=”b”></br>
<input type=”submit” value=”ADD” name=”add”>
</form>
<?
}
else
{
$c=$a+$b;
print “Addition of $a and $b is $c.”;
}
?>
</body>
</html>

HTML with PHP :-

HTML: add.htm

<html>
<head>
<title>Adding two numbers</title>
</head>
<body>
<form action=”add.php” method=”post”>
Enter the first number: <input type=”text” name=”a” size=10><br>
Enter the second number: <input type=”text” name=”b” size=10><br>
<input type=”submit” name=”submit” value=”ADD”>
</form>
</body>
</html>

PHP: add.php

<html>
<head>
<title>Adding two numbers</title>
</head>
<body>
<?php
$a=$_POST["a"];
$b=$_POST["b"];
$c=$a+$b;
print “Addition of $a and $b is $c.”;
?>
</body>
</html>

Only with PHP :-

<?php
$a = $_POST["a"];
$b = $_POST["b"];
if (!isset($_POST['add']))
{  // If page is not submitted to itself echo the form
?>
<html>
<head>
<title>Adding Two Numbers</title>
</head>
<body>
<form method=”post” action=”<?php echo $PHP_SELF; ?>”>
Enter the first number: <input type=”text” size=”12″ maxlength=”12″ name=”a”></br>
Enter the second number: <input type=”text” size=”12″ maxlength=”36″ name=”b”></br>
<input type=”submit” value=”ADD” name=”add”>
</form>
<?
}
else
{
$c=$a+$b;
print “Addition of $a and $b is $c.”;
}
?>
</body>
</html>


]]> http://www.biogem.org/2009/12/two-methods-to-run-php-script.html/feed 0 Linux wvdial.conf script for Vodafone IN http://www.biogem.org/2009/12/linux-wvdial-conf-script-for-vodafone-in.html http://www.biogem.org/2009/12/linux-wvdial-conf-script-for-vodafone-in.html#comments Tue, 08 Dec 2009 16:37:46 +0000 Ashok Kumar http://www.biogem.org/?p=135 [Modem0]
Modem = /dev/rfcomm0
Baud = 115200
SetVolume = 0
Dial Command = ATDT
Init1 = ATZ
Init3= ATM0
FlowControl = CRTSCTS
[Dialer vodafone]
Username = “vodafone”
Password = “vodafone”
Phone = *99#
Stupid Mode = 1
Init1 = ATZ
Init2 = ATQ0 V1 E1 S0=0 &C1 &D2 +FCLASS=0
Init3 = AT+CGDCONT=1,”10.10.1.100:9401″,”portalnmms”,”",0,0
Inherits = Modem0
[Dialer three]
Username = “none”
Password = “none”
Phone = *99#
Stupid Mode = 1
Init1 = ATZ
Init2 = ATQ0 V1 E1 S0=0 &C1 &D2 +FCLASS=0
Init3 = AT+CGDCONT=1,”10.10.1.100:9401″,”portalnmms”,”",0,0
Inherits = Modem0
[Modem0]
Modem = /dev/rfcomm0
Baud = 115200
SetVolume = 0
Dial Command = ATDT
Init1 = ATZ
Init3 = ATM0
FlowControl = CRTSCTS
[Dialer vodafone]
Username = “vodafone“
Password = “vodafone“
Phone = *99#
Stupid Mode = 1
Init1 = ATZ
Init2 = ATQ0 V1 E1 S0=0 &C1 &D2 +FCLASS=0
Init3 = AT+CGDCONT=1,”10.10.1.100:9401“,”portalnmms“,”",0,0
Inherits = Modem0
[Dialer three]
Username = “none“
Password = “none“
Phone = *99#
Stupid Mode = 1
Init1 = ATZ
Init2 = ATQ0 V1 E1 S0=0 &C1 &D2 +FCLASS=0
Init3 = AT+CGDCONT=1,”10.10.1.100:9401“,”portalnmms“,”",0,0
Inherits = Modem0


]]> http://www.biogem.org/2009/12/linux-wvdial-conf-script-for-vodafone-in.html/feed 4 Running C or C++ program in Linux http://www.biogem.org/2009/12/running-c-or-c-program-in-linux.html http://www.biogem.org/2009/12/running-c-or-c-program-in-linux.html#comments Fri, 04 Dec 2009 02:11:57 +0000 Ashok Kumar http://www.biogem.org/?p=90 Steps to run C program in Ubuntu:

1. Go to Applications > Accessories > Terminal, to open terminal window.

2. Type the following in command line

sudo gedit first.c

3. Enter the code bellow in the editor.

/* Program first.c */
#include<stdio.h>
main()
{
printf(”Hello World.\n”);
}

4. Save the file and close to return to terminal window.

5. Firstly compile the code using the following command

cc -c first.c

That would produce an object file you may need to add to the library.

6. Then create an executable using the following command

cc -o first first.c

7. Now run this executable using the following command

./first

8. Output should show as follows

Hello World.

Steps to run C++ program in Ubuntu:

1. Go to Applications > Accessories > Terminal, to open terminal window.

2. Type the following in command line

sudo gedit first.cpp

3. Enter the code bellow in the editor.

/* Program first.cpp */
#include<iostream>
main()
{
std::cout<<”Hello World.”<<std::endl;
}

4. Save the file and close to return to terminal window.

5. Now compile the code using the following command

g++ first.cpp -o second

6. Then run this executable using the following command

./second

7. Output should show as follows

Hello World.

A sample factorial program in C

/* Factorial using C */
#include<stdio.h>
int main()
{
int i,n,f=1;
printf(”\nEnter the number: “);
scanf(”%d”,&n);
for(i=1;i<=n;i++)
{
f=f*i;
}
printf(”\nFactorial of %d is %d \n\n”,n,f);
}

Output:

$ sudo gedit factorial.c
$ cc -c factorial.c
$ cc -o factorial factorial.c
$ ./factorial

Enter the number: 6
Factorial of 6 is 720

]]> http://www.biogem.org/2009/12/running-c-or-c-program-in-linux.html/feed 5 Addition using Perl/CGI in Ubuntu http://www.biogem.org/2009/12/addition-using-perlcgi-in-ubuntu.html http://www.biogem.org/2009/12/addition-using-perlcgi-in-ubuntu.html#comments Thu, 03 Dec 2009 03:26:03 +0000 Ashok Kumar http://www.biogem.org/?p=83 If Apache web server has installed in your system, you can run Perl/CGI script successfully. Create a html file and perl script using following steps.


Step 1: Creating a web page add.html

Open your console and type:

$ sudo gedit /var/www/add.html

Copy the lines below in the file and save it.

<html>
<head>
<title>Addition of two numbers.</title>
</head>
<body>
<br><br><br><br><br>
<form action=’cgi-bin/add.pl’ method=’post’ enctype=’multipart/form_data’>
<table border=’0′ align=’center’>
<tr><td colspan=’2′ align=’center’>
<b>Adding Two Numbers</b>
</td></tr>
<tr>
<td>Enter the first value:</td>
<td><INPUT TYPE =’text’ NAME=’n1′></td>
</tr>
<tr>
<td>Enter the second value:</td>
<td><INPUT TYPE =’text’ NAME=’n2′></td>
</tr>
<tr><td colspan=’2′ align=’center’>
<INPUT TYPE =’submit’ VALUE=’ADD’ NAME=’submit’>
</td></tr>
</table>
</form>
</body>
</html>


Step 2: Creating a perl script add.pl

Open your console and type:

$ sudo gedit /usr/lib/cgi-bin/add.pl
$ sudo chmod a+x /usr/lib/cgi-bin/add.pl

The command chmod a+x is used to allow permission to run the script. Without using this command your program will not run. !!!

Copy the lines below in the file and save it.

#!/usr/bin/perl -w
use CGI;
CGI::ReadParse();
$numb1 = $in{’n1′};
chomp($numb1);
$numb2 = $in{’n2′};
chomp($numb2);
$numb3=$numb1+$numb2;
CGI::PrintHeader();
print “content-type:text/html\n\n”;
print “<HTML>\n”;
print “<head><title>Addition of two numbers</title></head>\n”;
print “<body>\n”;
print “<br><br><br><br><br><center>Addition of $numb1 and $numb2 is $numb3.</center>\n”;
print “</body>\n”;
print “</html>\n”;


Step 3: Running the program

Open web browser and hit address http://localhost/add.html to run the Perl/CGI program.


]]> http://www.biogem.org/2009/12/addition-using-perlcgi-in-ubuntu.html/feed 5 Installing LAMP on Ubuntu 9.10 http://www.biogem.org/2009/11/installing-lamp-on-ubuntu-9-10.html http://www.biogem.org/2009/11/installing-lamp-on-ubuntu-9-10.html#comments Mon, 30 Nov 2009 02:40:33 +0000 Ashok Kumar http://www.biogem.org/?p=44

Installing and configuring LAMP (Linux, Apache, MySQL, and PHP) is easy in Ubuntu Linux. If you have internet connection in your system, you can able to download the necessary applications using apt-get or synaptic package manager tools.

In this tutorial, I have given step-by-step procedure to setup LAMP web server environment in Ubuntu 9.10 operating system.

Installing Apache:

The first application we will install is the web server Apache. To get started open your console and type:

sudo apt-get install apache2

Now enter the system password to download and install automatically. To test it, point your web browser to http://localhost/. If installation is successful, a text “It Works!” will display.

The location for saving webpages and script files are as follows.

Web Pages: /var/www
 Script Files: /usr/lib/cgi-bin
 Apache Configuration: /etc/apache2/sites-available

You can access the webpages using default address 127.0.0.1, system name, or localhost. If you wish to setup your own domain name, follow the steps bellow. (In this tutorial, i have chosen www.ashok.com as my domain name.)

sudo gedit /etc/hosts

Add “127.0.0.1         www.ashok.com” in the hosts file and save it. Now the problem is almost solved. To avoid errors in configurations, do the bellow steps too.

The first step is to make a copy of the original configuration file.

sudo cp /etc/apache2/sites-available/default /etc/apache2/sites-available/ashok.com

The second step is to change the configuration file to your own domain name.

sudo gedit /etc/apache2/sites-available/ashok.com

Add few lines in the configuration file (shown in blue color) as given bellow.

<VirtualHost *:80>

ServerAdmin webmaster@ashok.com
DocumentRoot /var/www
ServerName ashok.com
ServerAlias www.ashok.com

<Directory />
Options FollowSymLinks
AllowOverride None
</Directory>
:
:
.

The third step is to active new domain ashok.com and deactivate old domain.

sudo a2ensite ashok.com && a2dissite default

Finally restart the Apache web server.

/etc/init.d/apache2 reload

Your own domain name has been configured successfully.

Installing PHP:

The second application we will install is the PHP. To get started open your console and type:

sudo apt-get install php5 libapache2-mod-php5

Once this finishes we need to restart Apache. This will apply the changes.

sudo /etc/init.d/apache2 restart

Now let’s test it by replacing ‘/var/www/index.html‘ with index.php using command:

sudo cp /var/www/index.html /var/www/index.php

Replace the line with <?php phpinfo(); ?> in index.php file through an editor, using command ‘sudo /var/www/index.php‘. If PHP is installed properly, the page will display the information about installed modules of PHP.

Installing MySQL with PHP5:

Install all the MySQL stuff:

sudo apt-get install mysql-server libapache2-mod-auth-mysql php5-mysql

When you get a prompt enter a password you would like to use as the root MySQL user. Once done open, ‘sudo gedit /etc/mysql/my.cnf‘ and change the bind-address to your local IP. (Usually 192.x.x.x number). Note that this can be a security problem, because your database can be accessed by others computers than your own. Skip this step if the applications which require MySQL are running on the same machine.

Change the line bind-address = localhost to your own internal ip address ( e.g. 192.168.1.1 as bind-address = 192.168.1.1). If no need, skip this statement.

If your ip address is dynamic you can also comment out the bind-address line and it will default to your current ip.

Extra Stuff:

Installing phpMyAdmin:

All MySQL tasks including setting the root password and creating databases can be done via a graphical interface using phpMyAdmin or MySQL-Admin.

sudo apt-get install phpmyadmin

After phpMyAdmin is installed you can see it view it, http://localhost/phpmyadmin/.

User Name: phpmyadmin
 Password: your_password

Now, you have to grant permission to create or modify database. To do this you must be a super user (su). By default Ubuntu offers only sudo mode. To be safe, create new root password:

sudo passwd root

Keep the su password safely. It is needed to control every operations in Ubuntu. Remember that sudo and su password are different. !!!

Open your console and type:

su

/etc/init.d/mysql start

mysql -u root -p

mysql>GRANT ALL PRIVILEGES ON *.* TO ‘phpmyadmin@localhost’ IDENTIFIED BY ‘your_password’ WITH GRANT OPTION;

You can now able to create or modify tables through graphical interface of phpMyAdmin.

mod_rewrite:

Chances are you want to use mod_rewrite in your applications to make URLs a bit more pretty. It is also required by lots of webserver applications, like WordPress, Drupal, etc.

Do the following:

sudo a2enmod rewrite

/etc/init.d/apache2 restart

Method to Start / Stop Apache:

Use the following command to run Apache:

sudo /usr/sbin/apache2ctl start

To stop it, use:

sudo /usr/sbin/apache2ctl stop

To test configuration changes, use:

sudo /usr/sbin/apache2ctl configtest

Finally, to restart it, run:

sudo /usr/sbin/apache2ctl restart


]]> http://www.biogem.org/2009/11/installing-lamp-on-ubuntu-9-10.html/feed 31