Dockerfile

FROM ubuntu:16.04

MAINTAINER Raghu Chandramohan, Raghu.Chandramohan@bcm.edu

ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
ENV PATH /opt/conda/bin:$PATH

RUN apt-get update --fix-missing && \
    apt-get install -y wget bzip2 ca-certificates curl git && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*

RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh -O ~/miniconda.sh && \
    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
    rm ~/miniconda.sh && \
    /opt/conda/bin/conda clean -tipsy && \
    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

WORKDIR /opt

ENV TINI_VERSION v0.16.1
ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /usr/bin/tini
RUN chmod +x /usr/bin/tini

#ENTRYPOINT [ "/usr/bin/tini", "--" ]
#CMD [ "/bin/bash" ]

RUN git clone https://github.com/rghu/reconCNV.git && cd reconCNV && pip install --user --requirement requirements.txt

WORKDIR /opt/reconCNV/

RUN mkdir results

ENTRYPOINT ["python", "/opt/reconCNV/reconCNV.py"]
CMD ["-h"]