Dockerfile

FROM rocker/rstudio:latest-daily
MAINTAINER renatof@ufl.edu
RUN apt-get -y update
RUN apt-get -y install wget nano curl software-properties-common sudo git-core unzip gcc libgsl-dev libpng-dev libxml2-dev
USER rstudio
RUN cd /home/rstudio; wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh; bash Miniconda3-latest-Linux-x86_64.sh -b ; ./miniconda3/bin/conda init
ENV PATH="/home/rstudio/miniconda3/bin:$PATH"
RUN /home/rstudio/miniconda3/bin/conda install -c bioconda python-newick -y
RUN /home/rstudio/miniconda3/bin/conda install -c conda-forge pandas -y
RUN cd /home/rstudio; rm -rf msprime
RUN cd /home/rstudio; git clone --recurse-submodules https://github.com/tskit-dev/msprime.git
RUN cd /home/rstudio; cd msprime; pip install .
COPY install_packages.R /home/rstudio/install_packages.R
RUN cd /home/rstudio; Rscript /home/rstudio/install_packages.R
COPY .Rprofile /home/rstudio/.Rprofile
USER root
RUN chown rstudio:rstudio /home/rstudio/.Rprofile