Dockerfile

Dockerfile

# Docker container with Monocle3

FROM debian:latest

ARG NCORES=3

RUN apt-get update 
RUN apt-get install -y r-base-dev

ARG BIOC_INSTALL_ARGS="Ncpus=$NCORES, verbose=TRUE"
ARG R_INSTALL_ARGS="repos='https://cloud.r-project.org', $BIOC_INSTALL_ARGS"

RUN Rscript -e "install.packages( 'BiocManager', $R_INSTALL_ARGS )"

RUN Rscript -e "BiocManager::install( c( 'BiocGenerics', 'DelayedArray', 'DelayedMatrixStats', \
                       'limma', 'lme4', 'S4Vectors', 'SingleCellExperiment', \
                       'SummarizedExperiment', 'batchelor', 'HDF5Array', 'ggrastr' ), \
  					$BIOC_INSTALL_ARGS )"

RUN Rscript -e "install.packages( 'devtools', $R_INSTALL_ARGS )"
RUN Rscript -e "install.packages( 'remotes', $R_INSTALL_ARGS )"

RUN apt-get install -y libhdf5-dev

RUN Rscript -e "remotes::install_github( 'bnprks/BPCells/r', $BIOC_INSTALL_ARGS )"
RUN Rscript -e "remotes::install_github( 'cole-trapnell-lab/monocle3', $BIOC_INSTALL_ARGS )"