Software on Transit¶

Transit is an UPPMAX service that can be used to securely transfer files.

This page describes the software on Transit.

After logging 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.

SciLifeLab Data Delivery System - https://delivery.scilifelab.se/

# Load the tool from the software module tree
module load bioinfo-tools dds-cli

# Run the tool
dds

dds-cli

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.

2FA on transit

If you connect from abroad and you are asked for the 2FA (two factor authentication), there is a grace period (about 5 minutes) in which you can ssh/scp/rsync/sftp to transit without the need for 2FA. This allows you to use these and other tools that might experience problems with the 2FA.