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itmat / rum

RNA-Seq Unified Mapper
http://cbil.upenn.edu/RUM
MIT License
26 stars 4 forks source link

By default, don't log from read-only actions #42

Closed mdelaurentis closed 12 years ago

mdelaurentis commented 12 years ago

The following actions should be the only ones that actually print stuff to the log files by default:

These ones should not print to the log files (maybe unless the user gives a --debug option or something):

Some of the RUM modules log debug and info messages, which is good, but we should make it so that rum_runner initializes the logging system in a way that suppresses all log messages unless the action is align and possibly kill and clean. I'm not sure about kill and clean because they do affect the state of the pipeline, but they're probably not usually worth logging stuff.

mdelaurentis commented 12 years ago

I changed it so that rum_runner initializes the logging system only when the action is 'align' and we have an output directory. I didn't add --debug options or anything. That isn't really necessary now and can be done later if we have a need for it.