dataDownload.sh

#!/bin/bash

# download and extract raw data from SRA for microbiome analysis
# requires list of accession numbers (which should have associated metadata in another file, for later use)

cd `pwd`

#setting up silva reference file in silva directory
#download silva reference file version 128
#Mac
#curl https://www.mothur.org/w/images/b/b4/Silva.nr_v128.tgz -o Silva.nr_v128.tgz
#Linux
wget https://www.mothur.org/w/images/b/b4/Silva.nr_v128.tgz

#untar and gunzip silva reference file and send to directory
tar -zxvf Silva.nr_v128.tgz -C silva/
# remove tarball
rm *.tgz

#setting up data files and directories
mkdir data/SRP018246 data/SRP018247
#for Mac
#cut -f 6 data/SraRunTableSRP018246corrected.txt | tail +2 | sort > data/SRP018246.lst
#cut -f 6 data/SraRunTableSRP018247.txt | tail +2 | sort > data/SRP018247.lst
#for Ubuntu
cut -f 6 data/SraRunTableSRP018246corrected.txt | tail --lines=+2 | sort > data/SRP018246.lst
cut -f 6 data/SraRunTableSRP018247.txt | tail --lines=+2 | sort > data/SRP018247.lst

# download  Trachymyrmex/Cyphomyrmex
cd data/SRP018246
for x in `cat ../SRP018246.lst`
	do
		fastq-dump $x
done

# download Mycocepurus
cd ../SRP018247
for x in `cat ../SRP018247.lst`
	do
		fastq-dump $x
done