Dockerfile

FROM continuumio/anaconda3

COPY environment.yml /
RUN apt-get update && apt-get install -y procps && apt-get clean -y
RUN conda env create -f /environment.yml && conda clean -a
ENV PATH /opt/conda/envs/snpcall/bin:$PATH

# FROM broadinstitute/gatk:4.1.4.1
# 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 \
#     libglib2.0-0 libxext6 libsm6 libxrender1 \
#     git mercurial subversion
#
# RUN wget --quiet https://repo.anaconda.com/archive/Anaconda3-5.3.0-Linux-x86_64.sh -O ~/anaconda.sh && \
#     /bin/bash ~/anaconda.sh -b -p /opt/conda && \
#     rm ~/anaconda.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
#
# RUN apt-get install -y curl grep sed dpkg && \
#     TINI_VERSION=`curl https://github.com/krallin/tini/releases/latest | grep -o "/v.*\"" | sed 's:^..\(.*\).$:\1:'` && \
#     curl -L "https://github.com/krallin/tini/releases/download/v${TINI_VERSION}/tini_${TINI_VERSION}.deb" > tini.deb && \
#     dpkg -i tini.deb && \
#     rm tini.deb && \
#     apt-get clean
#
# ENTRYPOINT [ "/usr/bin/tini", "--" ]
# CMD [ "/bin/bash" ]
#