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 HTTPS:

wget -r -nH --cut-dirs=1 --no-parent -e robots=off  --no-check-certificate --reject="index.htm*"<run_name>/

NOTE: the trailing slash ("<run_name>/") is necessary to download only <run_name> and not the entire contents of ngsdata/

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, boslogin), you can use scp to copy files to your local computer:

scp -r <user_name><run_name> /path/to/my/directory

If transferring to another directory mounted on the FAS RC 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.