Dockerfile

FROM r-base:4.0.4

# Install required system components
RUN apt-get update && \
	apt-get install -y \
	libcurl4-openssl-dev \
	libssl-dev \
	libxml2-dev \
	libglpk-dev \ 
	libicu

# Create environment variables
ENV PATH=/opt/conda/condabin:/opt/conda/bin:${PATH}
ENV RENV_PATHS_ROOT=/root/project/renv
ENV RENV_PATHS_LIBRARY=/root/project/renv/library
ENV RETICULATE_MINICONDA_PATH=/opt/conda
ENV R_LIBS_SITE=/root/project/renv/library/R-4.0/x86_64-pc-linux-gnu:/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library

# Create arguments.  Values passed from docker-compose.yml
ARG SEURAT_VERSION=dev
ARG RENV_VERSION=0.13.2
ARG CONDA_VERSION=py38_4.9.2

# Add environment variables to Renviron
RUN echo "" >> ${R_HOME}/etc/Renviron
RUN echo "RENV_PATHS_ROOT=${RENV_PATHS_ROOT}" >> ${R_HOME}/etc/Renviron
RUN echo "RENV_PATHS_LIBRARY=${RENV_PATHS_LIBRARY}" >> ${R_HOME}/etc/Renviron
RUN echo "RETICULATE_MINICONDA_PATH=${RETICULATE_MINICONDA_PATH}" >> ${R_HOME}/etc/Renviron
RUN echo "R_LIBS_SITE=${R_LIBS_SITE}" >> ${R_HOME}/etc/Renviron

# Install miniconda
RUN mkdir -p /root/project
WORKDIR /root/project/
COPY environment.yml .

RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-${CONDA_VERSION}-Linux-x86_64.sh -O miniconda.sh && \
    mkdir -p /opt && \
    sh miniconda.sh -b -p /opt/conda && \
    ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
    echo ". /opt/conda/etc/profile.d/conda.sh" >> /root/.shinit && \
    echo "conda activate base" >> /root/.shinit && \
    find /opt/conda/ -follow -type f -name '*.a' -delete && \
    find /opt/conda/ -follow -type f -name '*.js.map' -delete && \
    conda update conda && \
    conda clean -afy  && \
    conda env create -f environment.yml && \
    echo ". /opt/conda/etc/profile.d/conda.sh" >> /root/.bashrc && \
    echo "conda activate r-reticulate" >> /root/.bashrc

# Install the renv package and install packages from lockfile
RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
RUN R -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"

# Restore R packages
WORKDIR /root/project/
COPY renv.lock .
COPY renv ./renv/
RUN R -e "renv::restore(lockfile='/root/project/renv.lock', library='/root/project/renv/library/R-4.0/x86_64-pc-linux-gnu')"

# Reinstall stringi due to issue with libicu, this is a work around because installing libicu-dev doesn't work
RUN R -e "install.packages('stringi')"

# Copy data
COPY data ./data/
COPY results ./results/
COPY rmarkdown ./rmarkdown/
COPY scripts ./scripts/

# Run R script
CMD ["Rscript", "--verbose", "./scripts/scMC_EC_new.R"]