getSRA

Wrapper bash scripts to download fastq files from SRA.
Instructions are for Mac or Linux OS.

Requirements

Download the sratoolkit binaries from here.
Make sure to choose the appropriate file for your system.

Place the sratoolkit package wherever you like and unzip it, as long as you know where the directory is.

# For example
# change directory to Documents
cd /Users/zktuong/Documents/

# make a folder called Softwares
mkdir Softwares

# go into the new folder
cd Softwares

# download
wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.6-1/sratoolkit.2.9.6-1-mac64.tar.gz

# unpack
tar -xzvf sratoolkit.2.9.6-1-mac64.tar.gz

# at this point, you can remove the original zip with
# rm sratoolkit.2.9.6-1-mac64.tar.gz

Installation and setup

Open up terminal/command line and navigate to the folder you want to download

# cd /Users/zktuong/Documents/Softwares
# this command will download this repository and create a folder called 'getSRA'
git clone https://github.com/zktuong/getSRA.git

We will point to the paths to the software by adding the paths into ~/.bashrc (or ~/.bashprofile).
Replace /<path>/<to>/ and <sratoolkit.version> accordingly.
In my example above, /<path>/<to>/ will become /Users/zktuong/Documents/Softwares/
and sratoolkit version will be sratoolkit.2.9.6-1.

echo 'export PATH=/<path>/<to>/getSRA/bin:$PATH' >> ~/.bashrc
echo 'export PATH=/<path>/<to>/<sratoolkit.version>/bin:$PATH' >> ~/.bashrc

# create a short cut to call getSRA.sh
echo 'alias getSRA="bash getSRA.sh -l "' >> ~/.bashrc

# reload
source ~/.bashrc

Usage

Download Accession list file from SRA run selector and place the file in the folder you want them to appear.

# cd /Users/zktuong/Downloads
getSRA SRR_Acc_List.txt

That's it! Enjoy!