An analysis pipeline for the purpose of investigating Carbapenemase-Producing Organisms.
This codebase is derived from the CPO_Prediction workflow, written by Justin Jia in collaboration with William Hsiao and Matt Croxen.
It is expected that several bioinformatics tools are provided as tool-specific conda environments. Each environment is activated in turn by calling:
source activate <tool-version>
...and deactivated by calling:
source deactivate
In order for this to work, a conda installation must be available on the user's PATH.
If these environments are not already available on your system, create them as follows:
conda create -n <tool-version> tool=version
For example:
conda create -n mash-2.0 mash=2.0