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Install ascp on Linux
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#!/bin/bash | |
## How to install ascp, in a gist. | |
## The URI below is not persistent! | |
## Check for latest link: https://www.ibm.com/aspera/connect/ | |
wget -qO- https://ak-delivery04-mul.dhe.ibm.com/sar/CMA/OSA/0a07f/0/ibm-aspera-connect_4.1.0.46-linux_x86_64.tar.gz | tar xvz | |
## run it | |
chmod +x ibm-aspera-connect_4.1.0.46-linux_x86_64.sh | |
./ibm-aspera-connect_4.1.0.46-linux_x86_64.sh | |
## add it to the path now and in the future | |
export PATH=$PATH:~/.aspera/connect/bin/ | |
echo 'export PATH=$PATH:~/.aspera/connect/bin/' >> ~/.bash_profile |
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#!/bin/bash | |
## Some helper functions to put in .bash_profile | |
# download SRR from NCBI SRA via Aspera Connect | |
# Usage: | |
# | |
# $ get-srr SRR304976 | |
# | |
get-srr () { | |
SRR=${1} | |
SRR_6=$(echo $SRR | cut -c1-6) | |
# Tune the ascp parameters for your bandwidth! | |
ascp -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh \ | |
-k 2 -T -l200m \ | |
anonftp@ftp.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/${SRR_6}/${SRR}/${SRR}.sra \ | |
. | |
} | |
# download all SRRs listed in a file | |
get-srr-all () { | |
while read srr; do | |
get-srr $srr | |
done <${1} | |
} |
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@hmkim yes, thanks. Since IBM apparently does not persist the download links, one almost always has to go through the site to get a working URL. I try to update the one in the Gist occasionally, but with NCBI phasing out aspera, I revisit this infrequently.