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# Ubuntu image as base
FROM ubuntu:18.04
# Install system dependencies
RUN apt-get update && apt-get install -y \
wget \
git \
libssl-dev \
libcurl4-openssl-dev \
libxml2-dev \
libxt-dev \
gdebi-core \
&& rm -rf /var/lib/apt/lists/*
# Set working directory
WORKDIR /root
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh && \
bash miniconda.sh -b -p /opt/miniconda && \
rm miniconda.sh
# Set environment variables for Conda
ENV PATH="/opt/miniconda/bin:$PATH"
# Create .condarc file for channel priority
RUN echo "channels:\n - conda-forge\n - bioconda\n - defaults\n - r" > /root/.condarc
# Create Conda environment and install dependencies
RUN conda create --name neuroestimator -y \
tensorflow=1.15.0 \
tensorflow-estimator=1.15.1 \
r-keras=2.3.0.0 \
r-tensorflow=2.2.0 \
h5py=2.10.0 \
hdf5=1.10.6 \
r-dplyr=1.0.9 \
r-base \
r-remotes \
'r-reticulate<=1.24'
# Activate environment and install NEUROeSTIMator
RUN /bin/bash -c "source activate neuroestimator && \
R -e 'remotes::install_git(\"https://research-git.uiowa.edu/michaelson-lab-public/neuroestimator\")'"
# Set entrypoint to bash
ENTRYPOINT ["/bin/bash"]