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Dockerfile
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FROM rocker/verse:3.4.3
MAINTAINER Manuele Simi "mas2182@med.cornell.edu"
LABEL org.opencontainers.image.source='https://github.com/MetaR-Languages/MetaR-DockerImage' \
Description='MetaR DockerImage' \
Vendor='Clinical and Translational Science Center at Weill Cornell Medicine' \
maintainer='Manuele Simi <mas2182@med.cornell.edu>' \
base_image='rocker/verse' \
base_image_version='3.4.3'
## Refresh package list and upgrade
## Remain current
RUN echo "deb http://ftp.us.debian.org/debian jessie main" >> /etc/apt/sources.list
RUN echo "deb-src http://ftp.us.debian.org/debian jessie main" >> /etc/apt/sources.list
#RUN echo "deb http://archive.ubuntu.com/ubuntu precise main universe" > /etc/apt/sources.list
RUN apt-get update
RUN apt-get -y --allow-unauthenticated install python-software-properties
RUN useradd docker \
&& mkdir /home/docker \
&& chown docker:docker /home/docker \
&& addgroup docker staff
RUN Rscript -e 'R.Version()'
RUN apt-get -y --allow-unauthenticated install libhdf5-dev
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("edgeR", ask=FALSE); biocLite("limma", ask=FALSE); ' \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds
RUN rm -rf /tmp/*.rds \
&& install2.r --error \
checkpoint \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds
## This is just to set a sane container wide default and is not required
RUN mkdir -p /etc/R \
&& touch /etc/R/Rprofile.site \
&& echo 'options(repos = list(CRAN = "http://cran.revolutionanalytics.com/"))' >> /etc/R/Rprofile.site
RUN mkdir -p /home/docker \
&& chown docker:docker /home/docker \
&& addgroup docker staff
RUN wget https://cran.r-project.org/src/contrib/hdf5r_1.0.1.tar.gz \
&& R CMD INSTALL hdf5r_1.0.1.tar.gz
ADD install-Seurat.R /tmp/install-Seurat.R
RUN Rscript --verbose /tmp/install-Seurat.R && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
ADD test.R test.R
ADD install-metaR-packages.R /tmp/install-metaR-packages.R
RUN Rscript --verbose /tmp/install-metaR-packages.R \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds
ADD install-metaR-packages-2.R /tmp/install-metaR-packages-2.R
RUN Rscript --verbose /tmp/install-metaR-packages-2.R \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds
ADD install-GLimma.R /tmp/install-GLimma.R
RUN Rscript --verbose /tmp/install-GLimma.R