Fixed tests
Updated matlab template
Matlab template fix
Updated source folder
Added Abaqus template
Fixing submission gateway on pan, used pan:pan.nesi.org.nz, now using gram.oua.nesi.org.nz
Details for diffs when test fails
Beast template that uses beagle
Fixed OpenBUGS tests
FSL files
Update INSTALL
Update README
update templates
Merge branch 'master' of github.com:nesi/applications

Updated the templates
Added java jobs
Added phyml
Added new tests
fixed checks for sandybridge/westmere requirements
More submit scripts for java sleep job
More submit scripts for java sleep job