Added new tools
Update docstring
Update tool names
Use binary absolute path in all tools
Add options for max mismatches and max matches
Leave job environment as default and use absolute path for binaries instead
Add tool to split Flux output by feature
Update flux split tool outputs and fix job names
Remove submodules
Clean up setup and add install target for make
Hack to remove duplicated log entries
Update develop make target
Update bundle make target
Update requirements
Fix format issue
Remove unused index tool
Fix hiding of options for the flux tool
Update modules buildout configuration
Add validate argument
Update tool definitions