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Dockerfile
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FROM rocker/verse:latest
LABEL maintainer="Yoshihiko Kunisato <kunisato@psy.senshu-u.ac.jp>"
# Install ipaexfont
RUN apt-get update
RUN apt-get install -y fonts-ipaexfont
# Insatall notofont
RUN apt-get install -y fonts-noto-cjk fonts-noto-cjk-extra
# install libjpeg & V8 for "psycho"
RUN apt-get install -y libjpeg-dev libv8-dev
# install ffmpeg
RUN apt-get -y install ffmpeg
# install ImageMagick++ library for magick
RUN apt-get install -y libmagick++-dev
# install clang for Rstan
RUN apt-get install -y clang make
# Install JAGS and other linux packages
RUN apt-get update && apt-get install -y \
jags \
libgsl0-dev \
tcl8.6-dev \
tk8.6-dev\
openmpi-bin\
libglpk-dev \
libcgal-dev \
libglu1-mesa-dev \
libsecret-1-dev \
libsodium-dev \
libssl-dev \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
# install sqlite3
RUN apt-get update
RUN apt-get install -y sqlite3
# install R packages
COPY install_r.r install_r.r
RUN ["r", "install_r.r"]
# install python packaegs
RUN apt-get install -y python3-pip
RUN pip3 install notebook \
jupyterlab \
jupyterlab-git \
jupyter_contrib_nbextensions \
lckr-jupyterlab-variableinspector \
scipy \
seaborn \
scikit-learn \
sympy \
mne \
axelrod \
deap \
japanize-matplotlib \
mecab-python3 \
unidic-lite \
networkx \
PuLP \
pymc3 \
simpy \
psychrnn \
pyddm \
inferactively-pymdp\
bokeh \
sudachipy
# Install Julia
ARG JULIA_VERSION="1.8.5"
RUN JULIA_MAJOR=`echo $JULIA_VERSION | sed -E "s/\.[0-9]+$//g"` && \
wget https://julialang-s3.julialang.org/bin/linux/x64/$JULIA_MAJOR/julia-$JULIA_VERSION-linux-x86_64.tar.gz && \
tar -xvzf julia-$JULIA_VERSION-linux-x86_64.tar.gz && \
cp -r julia-$JULIA_VERSION /opt/ && \
ln -s /opt/julia-$JULIA_VERSION/bin/julia /usr/local/bin/julia && \
rm -r julia-$JULIA_VERSION-linux-x86_64.tar.gz
RUN chown -hR rstudio:staff /opt/julia-$JULIA_VERSION
USER rstudio
RUN julia -e 'ENV["PYTHON"] = raw"/usr/bin/python3";using Pkg;Pkg.update();Pkg.add(["IJulia","PyCall"]);Pkg.build(["IJulia","PyCall"]);'
RUN julia -e 'using Pkg;Pkg.add(["DataFrames","PyPlot","Distributions","Statistics","JuliaFormatter","CPUTime","Gadfly","GLM","Optim","Plots","Query","RDatasets","SpecialFunctions","StatisticalRethinking","StatsBase","StatsFuns","StatsPlots","AdvancedHMC","BAT","Bijectors","CmdStan","DiffEqBayes","DistributionsAD","ForwardDiff","MCMCChains","MeasureTheory","ParameterizedFunctions","Turing","LinearAlgebra","DifferentialEquations","Roots","SymPy","ForneyLab"]);Pkg.precompile()'
USER root