Included with mastercoin-tools are 2 different methods for downloading/updating the blockchain information.

Continuous running application that you can start in a screen session. It will download/process the entire block chain and then sleep for 60 secs before checking for updates.:

screen -R msc
ctrl+a, d  <disconnect screen>

reconnect at anytime with
screen -R msc

Alternatively you can schedule a cron job to execute the utility at your predetermined time.