put OGS logs into cwd instead of SGE_BATCH_LOGDIR or ~
* Added ability to specify stiffness/weight/similarity for non linear minctracc calls through a protocol
Merge branch 'add-stiffness-etc' into develop
pyro4 upgrade and redesign of pydpiper main loops; various code improvements; some new bugs
fix shutdown logic
add changes from code review with Matthijs
Merge branch 'master' of github.com:mfriedel/pydpiper into develop
Merge branch 'improve_logging' of https://github.com/bcdarwin/pydpiper into ben_darwin_improve_logging
Merge branch 'ben_darwin_improve_logging' into develop
* merged changes from Ben Darwin regarding the location where OGS logs are stored.
Merge branch 'pyro4_upgrade' of https://github.com/bcdarwin/pydpiper into bcdarwin-pyro4_upgrade
Merge branch 'bcdarwin-pyro4_upgrade' into develop
* bumped version to 1.7. Added example parameters to the minctracc non linear protocol.
Merge branch 'release-1.7'