Download data from Caesar to Bianca

Modified on Tue, 29 Apr at 9:47 AM

To download data from Caesar to Bianca

1) Your public ssh key (in your laptop / local computer) should be sent to Clinical Genomics. In my case I specified my file ~/.ssh/id_ed25519.pub.

2) Use ssh-agent and agent forwarding to transfer the ssh key to the Transit server.

In my laptop:

start the ssh-agent if not started (for me it is automatically started when the laptop is started)

sudo ssh-add ~/.ssh/id_ed25519

(You can run the command “ssh-add -l” to list which keys are added to the agent.)

Connect to the transit server with flag -A to allow agent forwarding:

ssh -A username@transit.uppmax.uu.se

in transit, mount the project wharf:

mount_wharf sensXXXXXXX

(input password + second factor)

Cd to the project folder wharf which is now accessible:

cd sensXXXXXXX

In the project wharf, connect to Caesar:

sftp custXXX@caesar.scilifelab.se

Navigate to the correct folder on Caesar:

cd /home/custXXX/inbox

get -R YYYY

This will recursively download the content of the folder “YYYY” to the project wharf on Bianca.

If a download had to be interrupted (because it took longer than a day) it can be restarted with

reget -R YYYY