added in code for the monitoring
fixed bugs - ready to test tomorrow
made it so that is should continue from where it left off if script is rerun -- ready for testing
Merge pull request #1 from ICGC-TCGA-PanCancer/feature/ajw-add-monitoring

Feature/ajw add monitoring
Made it so that it uses the gtupload wrapper module
Update README.md
Merge pull request #2 from ICGC-TCGA-PanCancer/master

pulling in master to develop