Dockerfile.bladder

FROM r-base:4.4.1

ENV DEBIAN_FRONTEND=noninteractive

# Update package list and install required packages
RUN apt-get update && \
    apt-get install -y build-essential wget curl libcurl4-openssl-dev libxml2-dev \
    zlib1g-dev libssl-dev libbz2-dev libreadline-dev libsqlite3-dev libffi-dev

# Download and compile Python 3.10 with shared library support
RUN wget https://www.python.org/ftp/python/3.10.12/Python-3.10.12.tgz && \
    tar -xf Python-3.10.12.tgz && \
    cd Python-3.10.12 && \
    ./configure --enable-optimizations --enable-shared && \
    make -j$(nproc) && \
    make altinstall && \
    cd .. && \
    rm -rf Python-3.10.12.tgz Python-3.10.12

# Set Python 3.10 as default
RUN ln -s /usr/local/bin/python3.10 /usr/bin/python3 && \
    ln -s /usr/local/bin/pip3.10 /usr/bin/pip3

# Update library paths for Python shared library
RUN echo "/usr/local/lib" >> /etc/ld.so.conf.d/python3.10.conf && ldconfig

# Create a Python virtual environment
#RUN python3 -m venv /opt/venv
#RUN /opt/venv/bin/pip install --upgrade pip

# Set environment variables for reticulate
#ENV RETICULATE_PYTHON="/opt/venv/bin/python3"
ENV PYTHONPATH=/app#"${PYTHONPATH}:/app"
WORKDIR /app

# Set MPLCONFIGDIR to a writable directory and create it.
ENV MPLCONFIGDIR=/app/tmp/matplotlib
RUN mkdir -p /app/tmp/matplotlib

# installing r libraries
ADD coderbuild/bladder/requirements.R .
RUN Rscript requirements.R

# installing python libraries
ADD coderbuild/bladder/requirements.txt .
#RUN /opt/venv/bin/pip3 install -r requirements.txt
RUN pip3 install -r requirements.txt

RUN python3 --version
RUN which Rscript

#ENV PATH="/opt/venv/bin:$PATH"

ADD coderbuild/bladder/obtainGSMidLink.R ./
ADD coderbuild/bladder/CNV-segfile-annotation.R ./
ADD coderbuild/bladder/*py ./
ADD coderbuild/bladder/*sh ./

ADD coderbuild/utils/* ./