# Use the specified Micromamba base image with CUDA 11.7
FROM mambaorg/micromamba:2.1.1-cuda11.7.1-ubuntu20.04


USER root
ARG MAMBA_DOCKERFILE_ACTIVATE=1

# WORKDIR /home
# RUN mkdir -p /home/omic
WORKDIR /home/omic

# Install system packages
ARG DEBIAN_FRONTEND=noninteractive
RUN micromamba install -y python=3.9 pandas numpy && \
    pip install pandas numpy && \
    micromamba clean --all --yes

# Add the NVIDIA GPG key directly
RUN apt-get -y update \
    && apt-get install -y --no-install-recommends \
        build-essential \
        cmake \
        curl \
        git \
        wget \
        ca-certificates \
        hmmer \
        kalign \
        tzdata \
    && wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.0-1_all.deb \
    && dpkg -i cuda-keyring_1.0-1_all.deb && rm cuda-keyring_1.0-1_all.deb \
    && apt-get install -y --no-install-recommends cuda-command-line-tools-11-7 \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*


# Switch to the mamba user for micromamba operations
# USER $MAMBA_USER
# WORKDIR /home/omic

# Install Python and packages into the base environment

# Activate the base environment for subsequent RUN commands
# ARG MAMBA_DOCKERFILE_ACTIVATE=1

# # Install Python packages with pip (now runs in the activated environment)
# RUN python -m pip install pandas numpy

# Package into python script for running in nextflow
COPY drug_tissue_distribution.py /home/omic/drug_tissue_distribution.py
RUN chmod +x /home/omic/drug_tissue_distribution.py

# Copy reference files
COPY HPA_normal_ihc_data.tsv .
COPY MANE_all_transcipts.csv .
COPY digital_patient_extract_metrics.py .