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Dockerfile
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# Pull a base image
FROM ubuntu:20.04
# Copy everything (minus anything specified in .dockerignore) into the image
COPY . /opt/ECJ-2023-Suite-Of-Diagnostic-Metrics-For-Characterizing-Selection-Schemes
# To make installs not ask questions about timezones
ARG DEBIAN_FRONTEND=noninteractive
ENV TZ=America/New_York
##############################
# install base dependencies
# - for R repository
# - dirmngr
# - gpg-agent
# - for bookdown compilation
# - pandoc, pandoc-citeproc, texlive-base, texlive-latex-extra
##############################
RUN \
apt-get update \
&& \
apt-get install -y -qq --no-install-recommends \
software-properties-common \
curl \
g++-10 \
make\
cmake \
python3=3.8.2-0ubuntu2 \
python3-pip \
python3-virtualenv \
git=1:2.25.1-1ubuntu3 \
dirmngr \
gpg-agent \
pandoc \
pandoc-citeproc \
texlive-base \
texlive-latex-extra \
lmodern \
&& \
echo "installed base dependencies"
########################################################
# install r with whatever r packages we need/want
# - source: https://rtask.thinkr.fr/installation-of-r-4-0-on-ubuntu-20-04-lts-and-tips-for-spatial-packages/
########################################################
RUN \
gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
&& \
gpg -a --export E298A3A825C0D65DFD57CBB651716619E084DAB9 | apt-key add - \
&& \
apt update \
&& \
add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/' \
&& \
apt-get install -y -q --no-install-recommends \
r-base \
r-base-dev \
libssl-dev \
libcurl4-openssl-dev \
libfreetype6-dev \
libmagick++-dev \
libxml2-dev \
libfontconfig1-dev \
cargo \
&& \
R -e "install.packages('rmarkdown', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
R -e "install.packages('knitr', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
R -e "install.packages('bookdown', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
R -e "install.packages('tidyverse', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
R -e "install.packages('cowplot', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
R -e "install.packages('plyr', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
R -e "install.packages('Hmisc', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
R -e "install.packages('ggplot2', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
R -e "install.packages('dplyr', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
R -e "install.packages('PupillometryR', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
echo "installed r and configured r environment"
########################################################
# install osfclient, use to download project data
########################################################
RUN \
pip3 install osfclient \
&& \
export OSF_PROJECT=qz3g7 \
&& \
export PROJECT_PATH=/opt/ECJ-2023-Suite-Of-Diagnostic-Metrics-For-Characterizing-Selection-Schemes/DATA/ \
&& \
mkdir PROJECT_PATH \
&& \
osf -p ${OSF_PROJECT} fetch diagnostics-data.tar.gz ${PROJECT_PATH}diagnostics-data.tar.gz \
&& \
tar -xzvf ${PROJECT_PATH}diagnostics-data.tar.gz -C ${PROJECT_PATH} \
&& \
echo "download"
########################################################
# build supplemental material (will also run data analyses)
########################################################
RUN \
cd /opt/ECJ-2023-Suite-Of-Diagnostic-Metrics-For-Characterizing-Selection-Schemes/ \
&& \
ls -l \
&& \
cd /opt/ECJ-2023-Suite-Of-Diagnostic-Metrics-For-Characterizing-Selection-Schemes/Experiments/Base_Diagnostics/Bookdown \
&& \
chmod +x build_book.sh \
&& \
./build_book.sh \
&& \
echo "compiled bookdown base diagnostic ebook" \
&& \
cd /opt/ECJ-2023-Suite-Of-Diagnostic-Metrics-For-Characterizing-Selection-Schemes/Experiments/MVC_Diagnostics/Bookdown \
&& \
chmod +x build_book.sh \
&& \
./build_book.sh \
&& \
echo "compiled bookdown mvc diagnostic ebook" \
&& \
cd /opt/ECJ-2023-Suite-Of-Diagnostic-Metrics-For-Characterizing-Selection-Schemes/Experiments/Base_Scheme_Parameter_Sweep/Bookdown \
&& \
chmod +x build_book.sh \
&& \
./build_book.sh \
&& \
echo "compiled bookdown selection scheme sweep ebook" \
&& \
cd /opt/ECJ-2023-Suite-Of-Diagnostic-Metrics-For-Characterizing-Selection-Schemes/Experiments/MVC_Scheme_Parameter_Sweep/Bookdown \
&& \
chmod +x build_book.sh \
&& \
./build_book.sh \
&& \
echo "compiled bookdown selection scheme sweep mvc ebook" \
&& \
cd /opt/ECJ-2023-Suite-Of-Diagnostic-Metrics-For-Characterizing-Selection-Schemes/Experiments/Nondominated_Sorting_Contradictory_Objectives/Bookdown \
&& \
chmod +x build_book.sh \
&& \
./build_book.sh \
&& \
echo "compiled bookdown nondominated sorting parts on contradictory objectives ebook" \
&& \
cd /opt/ECJ-2023-Suite-Of-Diagnostic-Metrics-For-Characterizing-Selection-Schemes/ \
&& \
ls -Rl Books/ \