ocroci/complete repository overview

FROM rocker/r-ver:3.6.3

⁠#install needed libraries

RUN apt update &&
apt install -y libcurl4-openssl-dev libz-dev libtool python-dev libbz2-dev liblzma-dev libxml2-dev libxt6 libjpeg-dev libpng-dev libpcre3-dev libssl-dev && rm -rf /var/lib/apt/lists/* &&
R -e "install.packages(c('shiny','shinyFiles','shinydashboard','shinyWidgets','fastcluster','VennDiagram','data.table','RColorBrewer','ppcor','inline','BiocManager','RCurl'),repos='http://cran.us.r-project.org⁠')" &&
R -e "BiocManager::install(version = '3.9',ask=F)" &&
R -e "BiocManager::install('GenomicRanges', version = '3.9',ask=FALSE)" &&
R -e "BiocManager::install('Rsamtools', version = '3.9',ask=FALSE)" &&
R -e "BiocManager::install('rtracklayer', version = '3.9',ask=FALSE)" &&
R -e "BiocManager::install('compEpiTools', version = '3.9',ask=FALSE)"

RUN R -e "BiocManager::install('BSgenome.Mmusculus.UCSC.mm10',version = '3.9',ask=FALSE)" &&
R -e "BiocManager::install('TxDb.Mmusculus.UCSC.mm10.knownGene',version = '3.9',ask=FALSE)" &&
R -e "BiocManager::install('org.Mm.eg.db',version = '3.9',ask=FALSE)" &&
R -e "BiocManager::install('TxDb.Hsapiens.UCSC.hg19.knownGene',version = '3.9',ask=FALSE)" &&
R -e "BiocManager::install('org.Hs.eg.db',version = '3.9',ask=FALSE)" &&
R -e "BiocManager::install('TxDb.Hsapiens.UCSC.hg38.knownGene',version = '3.9',ask=FALSE)" &&
R -e "BiocManager::install('BSgenome.Mmusculus.UCSC.mm9',version = '3.9',ask=FALSE)"