FROM rocker/r-base:4.3.1

LABEL org.opencontainers.image.authors="Pasha Mazin <[email protected]>"

LABEL org.opencontainers.image.title="reticulate-free single cell format conversion"

LABEL org.opencontainers.image.description="Package to load scanpy h5ad into R as list, SingleCellExperiment or Seurat object."

LABEL org.opencontainers.image.source="https://github.com/cellgeni/schard"

LABEL org.opencontainers.image.licenses="MIT"

RUN apt-get update && \

apt-get install -y make zlib1g-dev libcurl4-openssl-dev libssl-dev \

libfontconfig1-dev libfreetype6-dev libfribidi-dev libharfbuzz-dev \

libjpeg-dev libpng-dev libtiff-dev pandoc libicu-dev libxml2-dev git \

libgit2-dev zlib1g-dev libicu-dev libcurl4-openssl-dev \

libglpk-dev libgmp3-dev libpng-dev python3

RUN Rscript -e 'install.packages(c("devtools","BiocManager"))'

RUN Rscript -e 'devtools::install_github("satijalab/seurat", "seurat5", quiet = TRUE)'

RUN Rscript -e 'BiocManager::install(c("rhdf5", "SingleCellExperiment"))'

RUN Rscript -e 'devtools::install_github("cellgeni/schard")'