Dockerfile_run

FROM python:3.7-slim-bullseye AS easel

ARG easel_version=0.48

RUN apt-get update && apt-get -y install \
    autoconf \
    build-essential
ADD https://github.com/EddyRivasLab/easel/archive/easel-${easel_version}.tar.gz easel.tar.gz
RUN tar xf easel.tar.gz
WORKDIR /easel-easel-${easel_version}
RUN autoconf && \
    ./configure && \
    make && \
    gcc -g -Wall -I. -L. -o esl_scorematrix \
        -DeslSCOREMATRIX_EXAMPLE \
        esl_scorematrix.c -leasel -lm && \
    cp esl_scorematrix /

# -----------------------------------------------------------------------------

FROM python:3.7-slim-bullseye as ultra

RUN apt-get update && apt-get -y install \
    zip \
    wget \
    build-essential \
    cmake

RUN wget https://github.com/traviswheelerlab/ultra/archive/545e0ce8058ca105d3a86e87bc6ef8b6862b5011.zip \
    && unzip /545e0ce8058ca105d3a86e87bc6ef8b6862b5011.zip \
    && mv /ULTRA-545e0ce8058ca105d3a86e87bc6ef8b6862b5011/ ULTRA/

WORKDIR /ULTRA
RUN cmake . && \
    make && \
    cp ultra /

# -----------------------------------------------------------------------------

FROM python:3.7-slim-bullseye as polya

RUN mkdir polyA
WORKDIR /polyA
RUN pip install pipenv

COPY Pipfile .
COPY Pipfile.lock .
RUN pipenv sync --python `which python` && \
    pipenv run pip freeze > /requirements.txt

# -----------------------------------------------------------------------------

FROM python:3.7-slim-bullseye

COPY --from=easel /esl_scorematrix /usr/local/bin/
RUN esl_scorematrix -h
COPY --from=ultra /ultra /usr/local/bin/
RUN ultra -h

RUN mkdir polyA
WORKDIR /polyA
COPY --from=polya /requirements.txt .
RUN pip install -r requirements.txt
COPY polyA/ polyA/

ENV PYTHONPATH=/polyA
ENTRYPOINT [ "python", "-m", "polyA" ]