Dockerfile

FROM debian:latest as builder

RUN apt-get update && apt-get install -y \
    openssh-client \
    git \
    && rm -rf /var/lib/apt/lists/*
COPY github_key .
RUN eval $(ssh-agent) && \
    ssh-add github_key && \
    ssh-keyscan -H github.com >> /etc/ssh/ssh_known_hosts && \
    git clone git@github.com:aidenlab/Polar.git /opt/Polar

FROM conda/miniconda3:latest    
LABEL maintainer="weisz@bcm.edu"

COPY --from=builder /opt/Polar /opt/Polar

RUN useradd -u 999 --user-group --system --create-home --no-log-init --shell /bin/bash -G sudo polar && \
    mkdir -p /tmp/test && ln -s /opt/Polar/test/fastq /tmp/test/fastq && \
    conda config --set always_yes yes --set changeps1 no && \
    conda update -q conda && \
    conda init bash && \
    conda env create -n Polar_cond_env -f /opt/Polar/Polar_conda_env.yml && \
    echo "source /usr/local/etc/profile.d/conda.sh\nPATH=/opt/Polar:\$PATH\nconda activate Polar_cond_env" >>/etc/profile.d/polar.sh && \
    conda clean --all -f -y

ENV BASH_ENV="/etc/profile.d/polar.sh"
ENV PATH=/opt/Polar:$PATH
SHELL ["/bin/bash", "--login", "-c"]
WORKDIR /fastq
ENTRYPOINT ["align_serial.sh"]