base.Dockerfile

FROM continuumio/miniconda3:4.11.0

ENV ENVIRONMENT=predector
ENV VERSION=1.2.7

LABEL maintainer="darcy.ab.jones@gmail.com"
LABEL description="Docker image containing all non-proprietary requirements for the predector pipeline"
LABEL pipeline.name="${ENVIRONMENT}"
LABEL pipeline.version="${VERSION}"

RUN apt-get update \
 && apt-get install -y procps libtinfo6 \
 && apt-get clean -y

ENV PATH="/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"

COPY environment.yml /
RUN chmod -R ugo+rws /opt \
 && conda env create --force -f /environment.yml \
 && conda clean -a --yes \
 && sed -i '/conda activate base/d' ~/.bashrc

ENV CONDA_PREFIX="/opt/conda/envs/${ENVIRONMENT}"
ENV PATH="${CONDA_PREFIX}/bin:${PATH}"
ENV PYTHONPATH="${CONDA_PREFIX}/lib/python3.9/site-packages:${PYTHONPATH}"

ENV CPATH="${CPATH}:${CONDA_PREFIX}/include"
ENV LIBRARY_PATH="${LIBRARY_PATH}:${CONDA_PREFIX}/lib"
ENV LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${CONDA_PREFIX}/lib"

# Needed for theano/deeploc
ENV CC="${CONDA_PREFIX}/bin/x86_64-conda_cos6-linux-gnu-cc"
ENV CXX="${CONDA_PREFIX}/bin/x86_64-conda_cos6-linux-gnu-c++"

CMD [ "/bin/bash" ]