weishwu/diffbind repository overview

FROM continuumio/anaconda3

WORKDIR /usr/share
RUN git clone https://github.com/vahidAK/NanoMethPhase.git
WORKDIR /usr/share/NanoMethPhase

RUN conda env create -f envs/environment.yaml

[weishwu@bfxcomp5-ap-ps1a docker_images]$ cat dockerfile_haven
FROM rocker/tidyverse

RUN Rscript -e "install.packages('haven')"

[weishwu@bfxcomp5-ap-ps1a docker_images]$ cat dockerfile_diffbind
FROM bioconductor/bioconductor_docker:RELEASE_3_15

RUN Rscript -e "install.packages(c(\  
        'cowplot', \
        'knitr', \
        'ggiraph', \
        'EnvStats', \
        'readxl', \
        'xlsx', \
        'ggforce', \
        'randomcoloR', \
        'RColorBrewer', \
        'pheatmap', \
        'Rtsne', \
        'umap', \
        'dplyr', \
        'ggplot2',\
        'ggpubr', \
        'hdf5r',\
        'patchwork',\
        'reticulate', \
        'grid', \
        'gridExtra', \
        'ggrepel', \
        'reshape2', \
        'tidyverse', \
        'tibble'));"

RUN wget -P /tmp https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.2-Linux-x86_64.sh && \
    sha256sum /tmp/Miniconda3-py37_4.8.2-Linux-x86_64.sh && \
    bash /tmp/Miniconda3-py37_4.8.2-Linux-x86_64.sh -p /miniconda -b && \
    rm /tmp/Miniconda3-py37_4.8.2-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 && \
    wget -P /tmp/ https://download1.rstudio.org/desktop/bionic/amd64/rstudio-1.2.5033-amd64.deb && \
    dpkg -i /tmp/rstudio-1.2.5033-amd64.deb

RUN apt-get install -y libboost-all-dev

RUN Rscript -e "BiocManager::install(c('DiffBind', 'csaw', 'profileplyr'))"