Feature/brian pancan fixes

Here's some information on before and after runtimes.  See the below for the particular templates to use to either 1) just install SeqWare or 2) build and install SeqWare.  Sergei can you try this out?

# new - 14 minutes
# vagrant_cluster_launch.seqware.install.sge_cluster.json.template
nohup time perl vagrant_cluster_launch.pl --use-aws --working-dir target-aws-install-sge-2-new --config-file vagrant_cluster_launch.seqware.sge_cluster.install.2node.json &>new.log

FINISHED!
14.99user 7.14system 20:21.74elapsed 1%CPU (0avgtext+0avgdata 353680maxresident)k
0inputs+10216outputs (0major+188411minor)pagefaults 0swaps

# old - 1 hour!
# vagrant_cluster_launch.seqware.sge_cluster.json.template
nohup time perl vagrant_cluster_launch.pl --use-aws --working-dir target-aws-install-sge-2-old --config-file vagrant_cluster_launch.seqware.sge_cluster.2node.json &>old.log

FINISHED!
13.68user 9.94system 1:00:30elapsed 0%CPU (0avgtext+0avgdata 347376maxresident)k
0inputs+48216outputs (0major+183060minor)pagefaults 0swaps