Using Aspera to Download Data

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.

From Windows, use MobaXterm (preferred) or PuTTY to connect to o2.hms.harvard.edu and make sure the port is set to the default value of 22.

From a Mac Terminal, use the ssh command, inserting your eCommons ID instead of user123:

1 ssh user123@o2.hms.harvard.edu

Start interactive job, and create working folder

1 2 3 4 5 6 7 8 9 10 11 # Start interactive job srun --pty -p interactive -t 0-12:0:0 --mem 2000MB -n 1 /bin/bash # 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. 

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 # 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

Download data use aspera follow the instructions from the data center. 

1 2 ascp ...


Additional tips: 

  1. If you need download a lot of data, run the screen command before starting an interactive job, to keep the session alive.

  2. 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!

  3. Contact us to let us know if you have any questions.