Dockerfile

FROM r-base:4.4.1

# install system dependencies
RUN  apt-get update && \
     apt-get install -y --no-install-recommends \
      liblzma-dev libbz2-dev libgsl-dev libcairo2-dev libpng-dev \
      build-essential libcurl4-openssl-dev libfftw3-dev libgfortran5  \
      libgmp3-dev libgraphviz-dev libgtk-3-dev libgtkmm-3.0-dev \
      libxml2-dev libssl-dev libunwind-dev libxt-dev pandoc libsvn1 \
      python3 python-is-python3 python3-dev python3-venv python3-pip \
      git curl  default-jdk libv8-dev \
      openjdk-17-jdk openjdk-17-jre \
      cargo libmagick++-dev libhdf5-dev


# install R packages
RUN R -e 'options(error=function(e)quit(status=2,save="no"),warn = 2); \
  install.packages(c("devtools","randomcoloR","knitr","doMC","RcppHungarian","hdf5r","reshape"),dependencies = TRUE,upgrade = "never");'

RUN R -e 'install.packages("BiocManager"); \
  options(error=function(e)quit(status=2,save="no"),warn = 2); \
  BiocManager::install(c("BSgenome.Mmusculus.UCSC.mm10","BSgenome.Hsapiens.UCSC.hg38","hexbin","clusterProfiler","org.Hs.eg.db","EBImage"),upgrade = "never");'

RUN R -e 'options(error=function(e)quit(status=2,save="no"),warn=2); \
  install.packages(c("fitdistrplus", "ggridges", "ica", "leiden", "lmtest", "pbapply", "RANN", "ROCR", "scattermore", "sctransform", "spatstat.explore", "spatstat.geom"));'

RUN R -e 'options(error=function(e)quit(status=2,save="no"),warn=2); \
  install.packages(c("Matrix","Seurat"));' 


RUN R -e 'options(error=function(e)quit(status=2,save="no"),warn = 2); \
  BiocManager::install(c("rhdf5"));'

RUN R -e 'options(error=function(e)quit(status=2,save="no"),warn=2); \
   devtools::install_github(c("cellgeni/visutils","iaaka/sajr"),upgrade = "never")'

COPY Dockerfile /docker/
RUN chmod -R 755 /docker

ENTRYPOINT []