move default root and log to commandline common
added root and log base to config recipies common and global
added root and log base to setup_global_configs
added root and log base to config recipes
added root and log base to toplevel tests
added root and log base to multiple toplevel tests
added root and log base to pipelines tests
move default database connect to commandline common
added database connect file to config recipes
added database connect file to pipeline tests
added database connect file to toplevel tests
added default database connect file to setup_global_configs
removed commented lines
updated usage text
updated usage text
tests use database config file
tidy added lines
Merge branch 'master' into base_root_and_log
pass additional params for single cell assembly
Merge pull request #44 from CraigPorter/base_root_and_log

Base root and log