Log file in case of failure

[fginter]

The stderr of the pipeline components should be redirected to a log file, whose location is shown to the user in case of failure. This should help us debug spurious failures of the parser.

[spyysalo]

May I suggest using the python logging system instead of print to stderr? It's really easy to get started with and quite flexible.

[fginter]

Most of the pipeline components are not even Python, but external programs. The stderr output needs to be gathered on the bash side. We do use Python logging module (occasionally ;).

[spyysalo]

Humbly withdrawn :-)