Monday, 5 May 2014

Install SRA toolkit on CentOS

1. Download SRA toolkit from

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
3. Add the below line in
    export PATH = $PATH:/softwares/sratoolkit.2.3.5-2-centos_linux64/bin
4. Save it and close
5. If you want to load the environment variables within without having to restart the machine, you can use the source command as in
     # source