Transit user guide

Transit

To facilitate secure data transfers to, from and within the system for computing on sensitive data (bianca/castor) a service is available via ssh at transit.uppmax.uu.se.

You can connect to transit via ssh. Once connected, you should see a short help message. The most important thing there is the

mount_wharf command

which you can use to mount a project from the bianca wharf, as in

username@transit:~$ mount_wharf sens2016001
Mounting wharf (accessible for you only) to /home/username/sens2016001
username-sens2016001@bianca-sftp.uppmax.uu.se's password: 
done.
username@transit:~$ ls sens2016001/
Desktop test
username@transit:~$ 

Note that your home directory is mounted read-only, any changes you do to your "local" home directory (on transit) will be forgotten afterwards.

You can use commands like rsync, scp and similar to fetch data and transfer it to your bianca wharf.

Moving data between projects

You can use transit to transfer data between projects by mounting the wharfs for the different projects and transferring data with rsync. Note that you may of course only do this if this is allowed (agreements, permissions, etc.)

Software on Transit

While logged in to Transit, you cannot make lasting changes to anything except for mounted wharf directories. However, anything you have added to your Rackham home directory is available on Transit. In addition, some modules are available.

For example, if you need to download data from TCGA, log in to Rackham and install the GDC client to your home directory. Then log in to Transit, mount the wharf, and run ./gdc-client.