How to Setup SRA Toolkit

Before we download any files from NCIB, there are a couple of preliminary setups one should install. Most of these files are going to be downloaded into your ssh server so make sure you have a designated server account to operate on.

If you have Windows PC trying to get on ssh server you will need PUTTY setup before proceeding.

Open your terminal. Make a new directory and go there using the:

mkdir sra_data #makes new directory

cd sra_data #goes to the new directory

To install SRA Toolkit, go to this link: https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit

and install the appropriate binaries for your OS. I use Ubuntu on Mac OS so will be using that as an example (command below):
```
wget --output-document sratoolkit.tar.gz https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz
```
Extract the file in the directory using the command below:
```
tar -vxzf sratoolkit.tar.gz
```
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 to home status
```
```
vi .profile # opends the editor to create PATH
```
Enter I key which the terminal screen will change into --Insert-- mode
Paste or input your path:
```
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.
Press Esc key to exit the insert mode.
Enter :wq to save your newly created path and exit the editor.
Once you are done saving the PATH and have exited the editor, enter source .profile in the terminal.