update-site.sh

 #!bin/bash

 cd /home/azureuser/
 git clone git@github.com:epiforecasts/covid-rt-estimates.git
 cd covid-rt-estimates
 sudo bash bin/update-docker.sh "build"
 sudo bash bin/update-via-docker.sh
 
FILE=last-update/update-complete
while [ ! -f "$FILE" ]; do
    echo "$FILE does not exist so keep waiting."
    sleep 60
done

echo "$FILE exists so updating GitHub and removing local estimates"

 git add --all
 git commit -m "update estimates"
 git push
 rm -r -f covid-rt-estimates

Add following to crontab using crontab -e to update every day at 7pm:

0 19 * * * /bin/bash /home/azureuser/update-site.sh >/dev/null 2>&1