weishwu/chipseeker repository overview

FROM bioconductor/bioconductor_docker:RELEASE_3_16

RUN Rscript -e "\
    BiocManager::install(c(\
        'EnsDb.Mmusculus.v109', \
        'EnsDb.Hsapiens.v109', \
        'clusterProfiler', \
        'ChIPseeker', \
        'ReactomePA', \
        'TxDb.Hsapiens.UCSC.hg38.knownGene')); \
    install.packages(c(\  
        'cowplot', \
        'dplyr', \
        'ggplot2',\
        'hdf5r',\
        'ggrepel', \
        'tidyverse'));"


RUN wget -P /tmp https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh && \
    sha256sum /tmp/Miniconda3-py39_4.12.0-Linux-x86_64.sh && \
    bash /tmp/Miniconda3-py39_4.12.0-Linux-x86_64.sh -p /miniconda -b && \
    rm /tmp/Miniconda3-py39_4.12.0-Linux-x86_64.sh

ENV PATH=/miniconda/bin:${PATH}

RUN mkdir -p /root/.local/share && \
    echo "/miniconda/bin/conda" > /root/.local/share/r-miniconda

RUN apt-get update && \
    apt-get install -y libxkbcommon-x11-0 && \
    apt-get install -y fonts-dejavu && \
    wget -P /tmp/ https://download1.rstudio.org/desktop/jammy/amd64/rstudio-2022.07.2-576-amd64.deb && \
    dpkg -i /tmp/rstudio-2022.07.2-576-amd64.deb

# based on quay.io/biocontainers/bioconductor-chipseeker:1.42.0--r44hdfd78af_0
BiocManager::install(c('ensembldb','AnnotationHub','org.Hs.eg.db','clusterProfiler'))