bash commands for downloading SRRs from NCBI's SRA

get-srr.sh

#!/bin/bash

# download SRR from NCBI SRA via Aspera Connect
#
# > get-srr SRR304976
get-srr () {
    SRR=${1}
    SRR_6=$(echo $SRR | cut -c1-6)
       
    ascp -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh \
      -k 2 -T -l 100m \
      anonftp@ftp.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/${SRR_6}/${SRR}/${SRR}.sra \
      .
}

# sequentially download all SRRs listed in a file
# e.g., Run Selector accession list
# 
# > get-srr-list SRR_Acc_List.txt
get-srr-list () {
    while read srr; do
	get-srr $srr
    done <${1}
}