Downloading many files by right-clicking each file in a webpage can be cumbersome. You can download all your files at once with the following commands
If downloading to your local computer, use wget to transfer files over HTTP:
wget -r -nH --cut-dirs=1 --no-parent -e robots=off --no-check-certificate --reject="index.htm*" https://data.rc.fas.harvard.edu/ngsdata/<run_name>
We use InCommon certificates that may or may not be part of the trusted authorities on your local machine, so --no-check-certificate may be necessary.
If you have credentials to login to an RC host (for example, rclogin03), you can use scp to copy files to your local computer:
scp -r <user_name>@rclogin03.rc.fas.harvard.edu:/n/boslfs/LABS/informatics/<run_name> /path/to/my/directory
If transferring to a directory mounted on the cluster, the best way to transfer files is with a copy command:
cp -r /n/ngsdata/<run_name> /path/to/my/directory
In all cases, replace <run_name> above with the name of the your sequencing run (e.g., 140523_D02345_1234_AH132DADXX), and <user_name> with your RC user name.