Merge pull request #37 from jrrideout/death-march

Glue
first pass at adding run() functionality
objects for configuration parsing
Merge branch 'death-march' of github.com:bipy/qcli into death-march
some changes to get logging working
working on cleaning up run() functionality
Merge pull request #38 from gregcaporaso/death-march

updates to get logging working
Merge pull request #39 from wasade/death-march

Death march
Make command-line parser work (maybe)
Merge branch 'death-march' of github.com:bipy/qcli into death-march

Conflicts:
	qcli/interface/cli.py