Dockerfile_R

FROM bioconductor/bioconductor_docker:RELEASE_3_18

MAINTAINER Jonas Schulte-Schrepping (jsschrepping)

# This will make apt-get install without question
ENV DEBIAN_FRONTEND noninteractive

RUN apt-get update && \
    apt-get install -y apt-utils \
		       pigz \
		       less \
		       lbzip2 
##################
### R PACKAGES ###

# install cran packages
ADD install_cran.R /installation/
RUN R -f /installation/install_cran.R

# install bioc packages
ADD install_bioc.R /installation/
RUN R -f /installation/install_bioc.R

# install bioc data bases
ADD install_biodb.R /installation/
RUN R -f /installation/install_biodb.R

# install github packages
ADD install_github.R /installation/
RUN R -f /installation/install_github.R
ADD install_github2.R /installation/
RUN R -f /installation/install_github2.R

# install scEpigenomics packages
ADD install_scEpi.R /installation/
RUN R -f /installation/install_scEpi.R

# install cytometry packages
ADD install_cyto.R /installation/
RUN R -f /installation/install_cyto.R

# install future packages
ADD install_future.R /installation/
RUN R -f /installation/install_future.R

# install future packages
ADD install_WGCNA.R /installation/
RUN R -f /installation/install_WGCNA.R

############
### TEST ###
RUN mkdir /logs

# list R packages
ADD test_installation.R /installation/
RUN R -f /installation/test_installation.R