# Docker image for project https://hub.stenci.la/elife/article-64846
# 
# Base this image on https://hub.docker.com/r/stencila/executa-midi
# which has Stencila executors, R and many R packages already installed
# Install additional packages required for this project.

FROM stencila/executa-midi:20210528.1

USER root
RUN Rscript -e 'install.packages(c("readxl","statmod","ggpubr","ggrepel","ggridges","ggplotify","reshape2","survival","survminer","pheatmap","ggraph","grid","devtools","RColorBrewer","weights","hexbin","BiocManager"))'
RUN apt-get update
RUN apt-get install -y libgsl-dev
RUN Rscript -e 'BiocManager::install(c("Biobase","GSVA","limma","GO.db","chromVAR","clusterProfiler","SummarizedExperiment","TxDb.Mmusculus.UCSC.mm10.knownGene","karyoploteR","org.Mm.eg.db","org.Hs.eg.db"))'
USER guest