Download python script and set it as executable:
chmod +x sra-download.py
Ensure that the environment python version is >= 3.4.
Install the SRA toolkit at https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit\_doc&f=std
Move the sratoolkit folder to /usr/bin, and add it to your environment using by appending export PATH=$PATH:/usr/bin/sratoolkit/bin to ~/.bash_profile
Install bwa (https://github.com/lh3/bwa) and ensure it is in your environment
Index the reference genome you intend to use with bwa index hg18.fa
sra-download.py [-h] [--pileup] reference acclist
reference: Reference genome file, must be indexed already
acclist: List of SRA sequences to be downloaded
--pileup: Combines bam output into pileup file. Requires samtools
Output will be sorted .bam files, found in the sra-download-out folder. If --pileup is used, output will be a single compiled.pl pileup file.