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want pypeflow's logger messages directed to a file #139

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dgordon562 opened this issue Jul 15, 2015 · 2 comments
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want pypeflow's logger messages directed to a file #139

dgordon562 opened this issue Jul 15, 2015 · 2 comments
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@dgordon562
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Is there a way to have pypeflow's logger messages sent to a file instead of stderr other than just doing it on the command line? Even better, can just logger info messages be sent to a file, and warning/fatal ones be sent to stderr?

@pb-cdunn
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Yes, that's all completely configurable. Look first at logging.ini in FALCON-examples. (Even if you aren't using that package, you can use the configuration there.) It sends some logging to stderr, above some level, and the more detailed logging (along with the less detailed) is split into 2 files, depending on the source.

For details on Python logging:

Currently, you pass logging.ini as the 2nd argument:

fc_run.py fc_run.cfg logging.ini

@pb-cdunn
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Added to FAQ.

pacbbbbot pushed a commit that referenced this issue Apr 24, 2018
…er to develop

* commit '790032c6023a2fd51949d63fdb05c5b2a6b483a0':
  The defaults of graph_to_contig.py now generate proper p_ctg and improper a_ctg, which should be the correct behaviour. The first read of an a_ctg is completely included in the collapsed region of the corresponding p_ctg right up until the fork.
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