Dockerfile.singularity

# Start from the rocker/tidyverse image for stable R and tidyverse installations
FROM satijalab/seurat:5.0.0

RUN apt-get update && apt-get upgrade -y && apt-get -f install -y 
# Install scDblFinder, and decontx dependencies 
RUN apt-get install -y \
    libpcre2-dev \
    libbz2-dev \
    zlib1g-dev \
    libglpk-dev \
    libharfbuzz-dev \
    libfribidi-dev \
    libcairo2-dev \
    libfreetype6-dev \
    libpng-dev \
    libtiff5-dev \
    libjpeg-dev

# Install system library for rgeos
RUN apt-get install -y libgeos-dev
# Install DoubletFinder
RUN R --no-echo --no-restore --no-save -e "remotes::install_github('chris-mcginnis-ucsf/DoubletFinder')"
# Install HoneyBADGER and InferCNV including dependencies
RUN apt-get update && apt-get install jags

RUN R --no-echo --no-restore --no-save -e "install.packages(c('rjags', 'infercnv'))"

RUN R --no-echo --no-restore --no-save -e "remotes::install_github('JEFworks/HoneyBADGER')"
# Install Harmony
RUN R --no-echo --no-restore --no-save -e "remotes::install_github('immunogenomics/harmony', force = TRUE)"
# Install faster Will coxon
RUN R --no-echo --no-restore --no-save -e "remotes::install_github('immunogenomics/presto', force = TRUE)"
# Install scDblFinder, and decontX
RUN R --no-echo --no-restore --no-save -e "BiocManager::install(c('scDblFinder', 'decontX'))"
# Install qs
RUN R --no-echo --no-restore --no-save -e "install.packages(c('qs'))"
RUN R --no-echo --no-restore --no-save -e "install.packages(c('stringr'))"
RUN R --no-echo --no-restore --no-save -e "install.packages(c('dplyr'))"
# Run Rscript
CMD ["Rscript"]