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Dockerfile
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FROM continuumio/miniconda3
## Get all the Linux dependencies
RUN apt-get update --fix-missing && \
apt-get install --yes \
wget \
curl \
bzip2 \
ca-certificates \
libglib2.0-0 \
libxext6 \
libsm6 \
libxrender1 \
git \
gcc \
g++ \
libreadline-dev \
libeigen3-dev \
tar \
build-essential && \
apt-get purge && \
apt-get clean
## Install Python dependencies
## NOTE: DO NOT install rpy2 from conda-forge, got issues
RUN pip install numpy scipy
## Install R and rpy2
RUN conda install -c r -y \
r-base=3.5.0 libiconv libxml2 lxml && \
pip install rpy2
RUN conda install -c conda-forge -y scikit-sparse
## Build TMB and it's dependencies
RUN R -e 'install.packages(c("Matrix", "numDeriv", "RcppEigen", "TMB"), repos="http://cran.us.r-project.org", dependencies=T)'
# && \
# cd /opt && \
# git clone https://github.com/kaskr/adcomp.git && cd adcomp && \
# make install-metis-full
## Install PyMB
RUN cd /opt && \
git clone https://github.com/sadatnfs/PyMB.git && \
cd PyMB && python setup.py install