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Dockerfile
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FROM us.gcr.io/dev-pipeline-internal/google-r-base:v1.0
## Copy the pipeline into the container
ADD ./ /BarcodeTender-pipeline/
## Resolving R and lib dependencies
RUN apt-get update \
&& apt-get install -y \
build-essential \
libbz2-dev \
libc6-dev \
libgcc-9-dev \
gcc-9-base \
liblzma-dev \
libssl-dev \
libxml2-dev \
libgit2-dev \
zlib1g-dev \
libcurl4-openssl-dev \
libhdf5-dev \
pandoc \
libpng-dev \
## clean up
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/
RUN Rscript -e 'install.packages("BiocManager");BiocManager::install("rhdf5")' \
&& Rscript -e 'install.packages(c("R.utils","rlang","assertthat","jsonlite"))' \
&& Rscript -e 'install.packages(c("data.table","Matrix","multimode"))' \
&& Rscript -e 'install.packages(c("dplyr","purrr","ggplot2","ids","DT"))' \
&& Rscript -e 'install.packages(c("optparse","rmarkdown"))'
RUN cd /BarWare-pipeline/ \
&& bash 00_setup.sh \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds