Dockerfile

############################################################
# Dockerfile to build chiron container
# Based on Ubuntu v23.04
############################################################

FROM python:3.10-slim
LABEL authors="Richard A. Schäfer"

# update sources list
RUN apt-get -y update && apt-get install -y
RUN apt-get install -y python3-dev build-essential python3-pip python3-setuptools python3-wheel tree
RUN apt-get install -y r-base libhdf5-dev
RUN pip3 install rdata
RUN pip3 install pandas
RUN pip3 install numpy
RUN pip3 install xgboost
RUN pip3 install scikit-learn
RUN pip3 install scikit-optimize
RUN pip3 install shap
RUN pip3 install matplotlib
RUN pip3 install openpyxl
RUN pip3 install optuna
RUN pip3 install pdbpp
RUN pip3 install pysnptools
RUN pip3 install vcfpy
RUN pip3 install configargparse

WORKDIR /usr/local/bin
ADD chiron /chiron
ADD ref /ref
RUN chmod +x /chiron/main.py

ENTRYPOINT [ "python3", "/chiron/main.py", "--input", "/input", "--output", "/output", "--ref", "/ref"]