Web Developers Portal

Monday 5 May 2014

Installing bedtools on centOS

1. Download bedtools from
https://github.com/arq5x/bedtools2/releases

2. Save it to a local folder (eg: softwares folder)
3. Untar it using below command

# tar xvzf bedtools-2.19.1.tar.gz

4. You can find all the bedtools function in bedtools-2.19.1/bin folder
5. You have to set the PATH environmental variable for bedtools so that OS can locate the bedtools program, even if it is not in the current directory

Setting PATH environmental variable for bedtools

1. Open /etc/profile.d
2. Create a document and name it as bedtools.sh
3. Add the below line in bedtools.sh
export PATH = $PATH:/softwares/bedtools-2.19.1/bin
4. Save it and close bedtools.sh
5. If you want to load the environment variables within bedtools.sh without having to restart the machine, you can use the source command as in
# source bedtools.sh

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