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sidbdri / cookiecutter-de_analysis_skeleton

Skeleton for new differential expression analysis project.
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issue with rmats dependency in system python3.8 #215

Closed hxin closed 1 year ago

hxin commented 1 year ago

https://github.com/sidbdri/cookiecutter-de_analysis_skeleton/blob/f02e83161035066085d553e7b9fbd2d53eee294c/%7B%7Bcookiecutter.project_name%7D%7D/rMATS.R#L129

we do not have all dependencies in the system python 3.8, thus we might need to switch to project VM before running the python command for rmats.

For example adding the following bit: export WORKON_HOME=${HOME}/.virtualenvs export PROJECT_HOME=${HOME}/projects export VIRTUALENVWRAPPER_PYTHON=/usr/bin/python3.8 source /usr/local/bin/virtualenvwrapper.sh workon xxxxxxxxxxx