Dockerfile

FROM us.gcr.io/dev-pipeline-internal/google-r-base:v2.0
RUN apt-get update \
    && apt-get install -y \
    gcc-9-base \
    libgcc-9-dev \
    libc6-dev \
    python3-pip \
    libbz2-dev \
    liblzma-dev \
    libssl-dev \
    libxml2-dev \
    libgit2-dev \
    zlib1g-dev \
    libcurl4-openssl-dev \
    libhdf5-dev \
    pandoc \
    libpng-dev \
    && Rscript -e "install.packages(c('BiocManager', 'devtools', 'assertthat', 'cowplot', 'data.table', 'viridis', 'plyr', 'dplyr', 'ids', 'ggplot2', 'jsonlite', 'Matrix', 'optparse', 'purrr', 'R.utils', 'rmarkdown')); \
      BiocManager::install('rhdf5'); \
      install.packages(c('leiden', 'png', 'reticulate')); \
      install.packages('Seurat', repos='http://cran.us.r-project.org'); " \
    ## clean up
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/ \
    && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
## Install AIFI Github packages
COPY auth_token /tmp/auth_token
RUN export GITHUB_PAT=$(cat /tmp/auth_token) \
   && R -e 'devtools::install_github("aifimmunology/H5weaver", auth_token = Sys.getenv("GITHUB_PAT")) ' \
  && git clone  https://aifi-gitops:$GITHUB_PAT@github.com/aifimmunology/tenx-rnaseq-pipeline.git \
  && rm -rf /tmp/downloaded_packages /tmp/*.rds /tmp/auth_token

#ENTRYPOINT ["tail", "-f", "/dev/null"]