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