A simple shell script to download samples from the SRA

downloadSRA.sh

#!/bin/bash

set -e
set -u
set -o pipefail

if ! `command -v fastq-dump > /dev/null 2> /dev/null`
then
    echo "Can't find fastq-dump!"
    exit 1
fi

if [[ "$#" -lt 1 ]]
then
    echo -e "\
Usage:  ./downloadSRA.sh sample_info [out_directory] \n\
Where:  'sample_info' is a list of SRA accessions to be downloaded \n\
\n\
        'out-directory' is an optional argument specifying where \n\
            to put downloaded files, defaulting to: \n\
            `pwd` \n\
" >&2
    exit 1
fi

SAMPLE_INFO=$1
OUTDIR=${2:-`pwd`}

#   Download reads from the SRA
#   --split-files   Split into forward and reverse files for paired end data
#   -I              Add _1 and _2 naming
#   -F              Use original sample naming within the file rather than SRA numbers
cd ${OUTDIR}
if `command -v parallel > /dev/null 2> /dev/null`
then
    parallel "fastq-dump -I --split-file -F {1}" :::: "${SAMPLE_INFO}" # Use the four dots to say 'read this file and use it as arguments'
else
    for sample in `cat "${SAMPLE_READS}"`
    do
        fastq-dump -I --split-files -F "$sample"
    done
fi