Web Developers Portal

Monday, 5 May 2014

Install SRA toolkit on CentOS

1. Download SRA toolkit from
http://eutils.ncbi.nih.gov/Traces/sra/?view=software

2. For centos 64 bit, we have to download sratoolkit.2.3.5-2-centos_linux64.tar.gz
3. Save it to a local folder (eg: softwares folder)
4. Untar it using below command

# tar xvzf sratoolkit.2.3.5-2-centos_linux64.tar.gz

5. You can find all the toolkit functions in the sratoolkit.2.3.5-2-centos_linux64/bin folder
6. You have to set the PATH environmental variable for toolkit so that OS can locate the fastq-dump program, even if it is not in the current directory

Setting PATH environmental variable for SRA Toolkit

1. Open /etc/profile.d
2. Create a document and name it as fastq-dump.sh
3. Add the below line in fastq-dump.sh
export PATH = $PATH:/softwares/sratoolkit.2.3.5-2-centos_linux64/bin
4. Save it and close fastq-dump.sh
5. If you want to load the environment variables within fastq-dump.sh without having to restart the machine, you can use the source command as in
# source fastq-dump.sh

Thursday, 24 April 2014

Add image/logo in browser tab for website

How to add image/logo in browser tab for website?

Place the below code under <head> tag in html

Monday, 24 February 2014

Installing xampp 1.8.3 on cent os 6.4

1. Download Xampp 1.8.3 for linux
2. Copy "xampp-linux-x64-1.8.3-3-installer.run" into Computer/Filesystem/opt folder
3. Open terminal from opt folder
4. Type below commands

[root@localhost opt]# chmod +x xampp-linux-x64-1.8.3-3-installer.run
[root@localhost opt]# ./xampp-linux-x64-1.8.3-3-installer.run

5. Window installation wizard will appear

6. Complete the installation process

Friday, 21 February 2014

Fatal server error: Cannot establish any listening sockets - Make sure an X server isn't already running

Issue

I have installed vncserver and when I tried to start it but I get the error below

"WARNING: The first attempt to start Xvnc failed, possibly because the font catalog is not properly configured. Attempting to determine an appropriate font path for this system and restart Xvnc using that font path ... Could not start Xvnc.

_XSERVTransSocketUNIXCreateListener: ...SocketCreateListener() failed _XSERVTransMakeAllCOTSServerListeners: server already running Warning: Xalloc: requesting unpleasantly large amount of memory: 0 bytes.

Fatal server error: Cannot establish any listening sockets - Make sure an X server isn't already running _XSERVTransSocketUNIXCreateListener: ...SocketCreateListener() failed _XSERVTransMakeAllCOTSServerListeners: server already running Warning: Xalloc: requesting unpleasantly large amount of memory: 0 bytes.

Fatal server error: Cannot establish any listening sockets - Make sure an X server isn't already running"

Solution

Terminate all VNCs processes. You can find the process number by running the following command:

#ps -e | grep vnc

11028 ? 00:00:00 Xvnc

kill the process using

#skill -p <pid>

#skill -p 11028

Reinstall vncserver

Tiger VNC on Centos 6.3 fails, font catalog not properly configured

Issue

Whe I try to set up Tiger VNC server on CentOS 6.3 but I'm getting the following error message when I run the command vncserver:

WARNING: The first attempt to start Xvnc failed, possibly because the font catalog is not properly configured. Attempting to determine an appropriate font path for this system and restart Xvnc using that font path ... Could not start Xvnc.

/usr/bin/Xvnc: symbol lookup error: /usr/bin/Xvnc: undefined symbol: pixman_composite_trapezoids

Solution

To resolve the above issue, run the below command in terminal

#yum install pixman pixman-devel libXfont

Installing VNCserver in centOS 6.4

1.    Installing GNOME Desktop

Install a window manager in order to get a full-featured GUI desktop

[root@localhost ~] #yum groupinstall "X Window System" "Desktop"

2.    Installing TightVNC Server

For CentOS 6, the server is: tigervnc-server not: vnc-server

[root@localhost ~] #yum install tigervnc-server

3.    Create a user and a vnc login

[root@localhost ~]# useradd tom

[root@ localhost ~]# passwd tom

Changing password for user tom .

New password:

Retype new password:

passwd: all authentication tokens updated successfully.

4.    Login to new user and set vnc password

[root@localhost ~]# su - tom

[tom@localhost ~]$ vncpasswd

Password:

Verify:

[tom@localhost ~]$ ls .vnc

passwd

[tom@localhost ~]$ exit

logout

5.    Start vnc

Create Xstartup Script by starting the vncserver

[root@localhost ~]# service vncserver start

Starting VNC server: 1:tom

New 'localhost.localdomain:1 (tom)' desktop is localhost.localdomain:1

Starting applications specified in /home/tom/.vnc/xstartup

Log file is /home/tom/.vnc/localhost.localdomain:1.log

[root@localhost ~]# su -l tom

[tom@localhost ~]$ ls .vnc

localhost.localdomain:1.log localhost.localdomain:1.pid passwd xstartup

[tom@localhost ~]$ exit

logout

6.    Edit the server configuration file

Edit /etc/sysconfig/vncservers, and add the following to the end of the file.

VNCSERVERS="1:tom"

VNCSERVERARGS[1]="-geometry 1024x768"

For multiple users repeat the steps 3 to 5 and add the user to the VNCSERVERS list and add a VNCSERVERARGS[x] entry.

So for two users:

VNCSERVERS="1:tom 2:john"

VNCSERVERARGS[1]="-geometry 1024x768"

VNCSERVERARGS[2]="-geometry 640x480"

7.    Open the port by editing the iptables

stop iptables

[root@localhost ~]# service iptables stop

open /etc/sysconfig/iptables

add the below lines before COMMIT

-A INPUT -p tcp -m state --state NEW -m tcp -m multiport --dports 5901:5910,6001:6010 -j ACCEPT

start iptables

root@localhost ~]# service iptables start

Install Vnc Viewer for remote accessing the desktop

1.    Download VNC Client

Now go to your Windows or Linux machine and download VNC Viewer client and install in your system to access the centos server desktop.

Download vnc viewer

2.    Connect to Remote Desktop(centos server) Using Client

After you installed the VNC Viewer client, open it you’ll get similar to below screen. Enter VNC Server IP address( IP address of centos server in which vncserver is installed) along with VNC ID (i.e 1) for user tom.

Uninstalling vncserver

[root@localhost ~]# service vncserver stop

[root@localhost~]#yum remove tigervnc-server

Sunday, 3 November 2013

localhost is not working in Xampp after updating Avast

Open Avast
1) Go to "Settings"
2) Go to "Troubleshooting"
3) Expand "Redirect Settings"
4) Under "WEB" look for ignored address
5) Add localhost
6) Open browser and visit your localhost page.

Sunday, 27 October 2013

Keep checkbox checked after submit refresh in PHP

Below code maintain checkbox value when user click preview button

<?php
if (isset($_POST['number']))
{
foreach ($_POST['number'] as $selectednumber)
$selected[$selectednumber] = "checked";
}
?>

<form action="" method="post">
<input type="checkbox" name="number[]" <?php echo $selected['one'] ?> value="one" />one<br />
<input type="checkbox" name="number[]" <?php echo $selected['two'] ?> value="two" />two<br />
<input type="checkbox" name="number[]" <?php echo $selected['three'] ?> value="three" />three<br />
<input type="checkbox" name="number[]" <?php echo $selected['four'] ?> value="four" />four<br />

<input type="submit" name="Submit" value="Preview" />
</form>

Friday, 25 October 2013

How to get previous page url in PHP

$realname = basename($_SERVER['HTTP_REFERER'], ".php");

Multiple submit button in a single form in PHP

Thursday, 24 October 2013

Installing the Java Plugin for Firefox on CentOS

The OpenJDK bundled with CentOS is missing a java plugin for Firefox. A simple method of getting Java to run inside the webbrowser and to run java applications is to install icedtea-web

Open a terminal and type the below command

yum install icedtea-web

Then restart your browser
Click Tools- >Add-ons
The Add-ons Manager tab will open.
In the Add-ons Manager tab, select Plugins
Click icedtea-web plugin to select it and click on the Enable button

The java verification applet (http://www.javatester.org/version.html) works fine.

Installing and configuring Java in cent OS

Most of the Linux operating systems comes with pre-installed OpenJDK package to run java-based applications and plugins.But in certain cases we need Sun/Oracle Java program to compile and run
particular development applications.

1. Download java from
http://www.oracle.com/technetwork/java/javase/downloads/index.html

2. install java using rpm -uvh
## Install Java on 32-Bit OS ##
# rpm -Uvh jdk-7u45-linux-i586.rpm
# rpm -Uvh jdk-7u45-linux-i586.rpm

## Install Java on 64-Bit OS ##
# rpm -Uvh jdk-7u45-linux-x64.rpm
# rpm -Uvh jdk-7u45-linux-x64.rpm

3. check java installed
# java -version

output should be
java version "1.7.0_45"

4. Setting up java environment variables
The easiest way to set an environment variable in CentOS is to use export as in

$> export JAVA_HOME=/usr/java/jdk.1.7.0_45

$> export PATH=$PATH:$JAVA_HOME

However, variables will disappear the moment you exit the shell. Obviously this is not helpful when setting environment variables that need to persist even when the system reboots.In such cases, you need to set the variables within the system wide profile. In CentOS , the folder /etc/profile.d/ is the recommended place to add customizations to the system profile.

5. Create a new file called java.sh
vim /etc/profile.d/java.sh

6. Copy paste the below content in java.sh

export JRE_HOME=/usr/java/jdk.1.7.0_45/jre
export PATH=$PATH:$JRE_HOME/bin
export JAVA_HOME=/usr/java/jdk.1.7.0_45
export JAVA_PATH=$JAVA_HOME
export PATH=$PATH:$JAVA_HOME/bin

7. If you want to load the environment variables within java.sh without having to restart the machine, you can use the source command as in:
$> source java.sh

Wednesday, 23 October 2013

Add horizontal scrollbar to html table

Inorder to add a horizontal scroll bar on html table automatically as the table grows, we need to wrap the table inside a div and add overflow:auto css property

For eg:

Friday, 4 October 2013

Fatal error: Call to undefined function http_redirect() : Fixed

Issue: When I was trying to call the PHP http_redirect() function, below error came up:

Fatal error: Call to undefined function http_redirect() in location.

Add the below function in your php page
/**
* redirect to a specific URL
* @param $url
*/
     function redirect($url)
{
     if (!headers_sent())
     {
          //If headers not sent yet... then do php redirect
          header('Location: '.$url); exit;
     }
     else
     {
          //If headers are sent... do javascript redirect...
          //if javascript disabled, do html redirect.
          echo '<script type="text/javascript">';
          echo 'window.location.href="'.$url.'";';
          echo '</script>';
          echo '<noscript>';
          echo '<meta http-equiv="refresh" content="0;url='.$url.'" />';
          echo '</noscript>'; exit;
     }
}

then call the above function to the page you wish the redirect to happen on

eg: redirect("redirect.php");

Friday, 12 July 2013

Cannot access xampp from internet in Cent OS

Issue

I have xampp installed on Cent OS. I started the xampp server and tried to access it with localhost, it is working. But i cant access it using the system IP. I can ping the server.But I can't access the server from any other computer on the network.

Solution

The default firewall of CentOS permits ssh input(tcp 22) and icmp(ping). Open a terminal and type

[root@ ~]# cat /etc/sysconfig/iptables
# Firewall configuration written by system-config-firewall
# Manual customization of this file is not recommended.
*filter
:INPUT ACCEPT [0:0]
:FORWARD ACCEPT [0:0]
:OUTPUT ACCEPT [0:0]
-A INPUT -m state --state ESTABLISHED,RELATED -j ACCEPT
-A INPUT -p icmp -j ACCEPT
-A INPUT -i lo -j ACCEPT
-A INPUT -m state --state NEW -m tcp -p tcp --dport 22 -j ACCEPT
-A INPUT -j REJECT --reject-with icmp-host-prohibited
-A FORWARD -j REJECT --reject-with icmp-host-prohibited
COMMIT

Try at first stopping your firewall issuing the following command:

[root@ ~]# /etc/init.d/iptables stop

Now, test if you can access your XAMPP server.
Go to File System -> etc - >sysconfig
Open iptables. Remove the below line

-A INPUT -j REJECT --reject-with icmp-host-prohibited

Add the below new line

iptables -A INPUT -m state --state NEW -m tcp -p tcp -m multiport --dports 80,443 -j ACCEPT

It enables the ports you need to access(80 , 443).
Now your iptables looks like

# Firewall configuration written by system-config-firewall
# Manual customization of this file is not recommended.
*filter
:INPUT ACCEPT [0:0]
:FORWARD ACCEPT [0:0]
:OUTPUT ACCEPT [0:0]
-A INPUT -m state --state ESTABLISHED,RELATED -j ACCEPT
-A INPUT -p icmp -j ACCEPT
-A INPUT -i lo -j ACCEPT
-A INPUT -m state --state NEW -m tcp -p tcp --dport 22 -j ACCEPT
-A INPUT -m state --state NEW -m tcp -p tcp -m multiport --dports 80,443 -j ACCEPT
-A FORWARD -j REJECT --reject-with icmp-host-prohibited
COMMIT

Save the file and close it.
Start your firewall issuing the following command:

[root@ ~]# /etc/init.d/iptables start

Now you can access your XAMPP server using your macine ip address