Aspera is a tool that can be leveraged to quickly and efficiently download data. This page details how to install Aspera and so you can use it to download files as needed.Due to Aspera license limitations, cluster users have to install the software under their home directory to use it.
Log on to O2
If you need help connecting to O2, please review the How to login to O2 wiki page.
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ssh user123@o2.hms.harvard.edu
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Log in to transfer cluster and create working folder
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# Start interactive job
srun --pty -p interactive -t 0-12:0:0 --mem 2000MB -n 1 /bin/bash
ssh transfer
# Make a scratch3 directory for aspera
# This assumes you have a scratch directory already
# "{USER:0:1}" will be replaced by the first letter of your eCommons
# $USER will be replaced by your eCommons
mkdir /n/scratch3/users/${USER:0:1}/$USER/testAspera
# change to the test directory for aspera
cd /n/scratch3/users/${USER:0:1}/$USER/testAspera |
Download aspera and install it. You only need to do this once.
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# Download the aspera software # You can check the aspera website for the latest version of the tool.
# The command below downloads the version that was the most recent when this page was initially written
wget https://download.asperasoft.com/download/sw/connect/3.9.1/ibm-aspera-connect-3.9.1.171801-linux-g2.12-64.tar.gz
# Decompress
tar -xvzf ibm-aspera-connect-3.9.1.171801-linux-g2.12-64.tar.gz
# Install it
sh ibm-aspera-connect-3.9.1.171801-linux-g2.12-64.sh
# Setup software license
mkdir -p ~/.ssh; ln -s ~/.aspera/connect/etc/asperaweb_id_dsa.openssh ~/.ssh/
# Setup path
export PATH=~/.aspera/connect/bin:$PATH
# To make sure the path is automatically available once you login later on, add the command to ~/.bashrc
echo export PATH=~/.aspera/connect/bin:\$PATH >> $HOME/.bashrc
# Make sure the ascp command is available now
which ascp
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Download data use aspera follow the instructions from the data center.
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If you need download a lot of data, run the screen command before starting an interactive jobssh to transfer cluster, to keep the session alive.
If you have more than a dozen samples to download, running downloads one by one requires a lot of time. You can run them in parallel instead. For example you can submit 5 jobs, but let each job download 100 samples. If you try this method, please share your experience with us. We are always happy to hear feedback and to modify our documentation and recommendations accordingly!
Contact us to let us know if you have any questions.