FROM continuumio/anaconda3:2021.05

RUN apt-get update --allow-releaseinfo-change \
 && apt-get install -y \
    g++ \
    cmake \
    zlib1g-dev \
    libbz2-dev \
    bc \
    libtbb2

# 'cd' into the build directory is required !
RUN wget http://cab.spbu.ru/files/release3.15.3/SPAdes-3.15.3.tar.gz \
 && tar -xzf SPAdes-3.15.3.tar.gz \
 && rm SPAdes-3.15.3.tar.gz \
 && cd /SPAdes-3.15.3 \
 && ./spades_compile.sh

ENV PATH="/SPAdes-3.15.3/bin:${PATH}"

RUN conda install -c bioconda \
    cd-hit=4.8.1 \
    hmmer=3.3.2 \
    bowtie2=2.4.1 \
    samtools=1.11 \
    bedtools=2.30.0 \
 && conda clean --all --yes

RUN pip install --no-cache-dir \
    numpy==1.19.2 \
    pandas==1.2.4 \
    matplotlib==3.3.2 \
    seaborn==0.11.0 \
    scipy==1.5.2 \
    statsmodels==0.12.0 \
    argparse==1.1

COPY ./MetaGPA/* /MetaGPA/MetaGPA/
COPY ./__main__.py /MetaGPA/

WORKDIR /
ENTRYPOINT ["python", "MetaGPA"]