zairachem-docker

To install ZairaChem v2 do the following:

git clone https://github.com/ersilia-os/zairachem-docker
cd zairachem-docker
bash install.sh

This will create a conda environment for each step of the processing pipeline.

Model fitting

bash run_fit.sh -i [INPUT_FILE] -m [MODEL_DIR]

Optional flags for the fit command include:

-c|--cutoff <float>
-d|--direction high/low
-p|--parameters <parameters_file.json>
--clean True/False
--flush True/False
--anonymize True/False

If no cut-off and direction is passed the file must contain a column with the data already binarized

Model predicting

bash run_predict.sh -i [INPUT_FILE] -m [MODEL_DIR] -o [OUTPUT_DIR]

Optional flags for the fit command include:

--clean True/False
--flush True/False
--anonymize True/False