Configuring ssh for GenBank Alignments

Due to the fact that rsh does not return the exit code of the remote process, ssh is used to run remote processes. In order for this to run unattended, ssh must be configured to run without prompting for a password. Authentication of ssh with .rhosts is not enabled at UCSC, so setting up a no passphrase key is the easiest way to achieve this.

  1. Generate a key without a passphrase.
          ssh-keygen -t dsa -f ~/.ssh/nokey_dsa -N ''
          
  2. Copy the contents on .ssh/nokey_dsa.pub to .ssh/authorized_keys.
  3. Modify .ssh/config to specify using this identity file:
          Host *
                  IdentityFile ~/.ssh/nokey_dsa
                  IdentityFile ~/.ssh/id_dsa
          
  4. Verify that you can ssh from kkstore to kk, If you are using ssh-agent, exit it before testing.
          ssh kk uname -a
          
  5. If you have started an alignment and discover that the ssh is not working correctly, fix the problem and restart gbAlignStep process by adding the -continue=copy option. This restarts that process at the point of copying the files to the iservers. All other options will be the same.