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RahmanTeamDevelopment / CoverView

A coverage and base/mapping quality evaluation tool for panel and whole exome next-generation sequencing
MIT License
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Unset $PYTHONPATH when running CoverView #2

Closed andyrimmer closed 7 years ago

andyrimmer commented 7 years ago

If the PYTHONPATH environment variable is set then this can over-ride the module search paths used by virtualenv. This can cause all kinds of nasty and hard-to-understand run-time problems when python grabs the wrong version of e.g. pysam.

To avoid this, CoverView should be run through a thing wrapper script which removes the PYTHONPATH variable in the sub-shell that runs CoverView. The wrapper script should be placed in env/bin/coverview.

andyrimmer commented 7 years ago

I've added a wrapper script bin/coverview that unsets PYTHONPATH and then runs CoverView.py.