FROM ubuntu:latest

ARG DEBIAN_FRONTEND=noninteractive
USER root

# Install gradle and JDK
RUN apt -y update && apt-get -y update
RUN apt install -y build-essential openjdk-8-jdk wget git python3 python3-pip tabix

# install conda
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh && \
    mkdir -p /opt && \
    sh miniconda.sh -b -p /opt/conda && \
    rm miniconda.sh && \
    ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
    echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
    echo "conda activate base" >> ~/.bashrc && \
    find /opt/conda/ -follow -type f -name '*.a' -delete && \
    find /opt/conda/ -follow -type f -name '*.js.map' -delete && \
    /opt/conda/bin/conda clean -afy

ENV PATH /opt/conda/bin:$PATH

# main conda env (synthea)
RUN conda create -n synthea
ENV PATH "$PATH:/opt/conda/envs/synthea/bin"
RUN echo "source activate synthea" >> ~/.bashrc

# Install pandas and numpy
RUN python3 -m pip install --upgrade pip
RUN python3 -m pip install pandas numpy fuzzywuzzy python-Levenshtein requests

# Install synthea from latest release
RUN wget https://github.com/synthetichealth/synthea/archive/refs/tags/master-branch-latest.tar.gz
RUN tar xzf master-branch-latest.tar.gz && mv synthea-master-branch-latest synthea
WORKDIR /synthea

ARG PATH $PATH:/synthea
ENV PATH $PATH:/synthea

RUN conda config --add channels bioconda
RUN conda config --add channels conda-forge

# Install samtools
RUN conda install -n synthea -c bioconda samtools

# Install UCSC Liftover
RUN conda install -n synthea -c bioconda ucsc-liftover
RUN conda install -n synthea -c bioconda gatk4
RUN conda install -n synthea -c bioconda bedtools
RUN apt-get -y install vcftools

# DNA to Protein Sequence code
WORKDIR /synthea
RUN git clone https://github.com/prestevez/dna2proteins.git
RUN mv dna2proteins/dna2proteins.py .
RUN rm -r dna2proteins
RUN apt install -y 2to3
RUN 2to3 -w dna2proteins.py

#Test
# RUN ./gradlew build check test
RUN ./run_synthea -p 10 --exporter.csv.export true
# use -a for age range e.g. 30-40 and -g for gender M/F