Aspera is a tool that can be leveraged to quickly and efficiently download data. This page details how to use it to download files as needed.
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:
ssh user123@o2.hms.harvard.edu |
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 |
ascp -i /opt/aspera/etc/asperaweb_id_dsa.openssh ... |
If you need download a lot of data, run the screen command before ssh 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!