Once the file extraction is complete, to properly execute the toolkit, create a PATH environment in the terminal using the following command:
cd (goes back home)
vi .profile (opens the editor)
Press I key and then hit Enter.
The terminal screen will change into — Insert — mode.
Paste or input your path. For me it will look like this:
export PATH=/home/compbio/sra_data/sratoolkit.3.0.1-ubuntu64/bin:$PATH
Note: Make sure you are correctly entering the pathway where your toolkit is installed. Notice the end of the directory for the toolkit is bin where the software tools e.g. fastq-dump are located.