Install ascp on Linux

install-ascp.sh

#!/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

util_functions.sh

#!/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 \
	 [email protected]:/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}
}

@Shicheng-Guo no, you need to use the one included in the ascp installation. It should be at .aspera/connect/etc/asperaweb_id_dsa.openssh, which installs to the user home if following the install script I provided.

Download a connector from https://www.ibm.com/aspera/connect/

@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.