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Revise docker to pull from intro to R #59

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Jul 3, 2024
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Revise docker to pull from intro to R #59

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73 changes: 2 additions & 71 deletions docker/Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,76 +1,7 @@
FROM rocker/tidyverse:latest
FROM jhudsl/intro_to_r:1.1.1
LABEL maintainer="[email protected]"
WORKDIR /rocker-build/

# Install apt-getable packages to start
RUN apt-get update && apt-get install -y --no-install-recommends apt-utils dialog
RUN apt-get install -y --no-install-recommends \
libxt6 \
libpoppler-cpp-dev \
vim \
libglpk40 \
curl \
gpg

# Install gh
RUN curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | gpg --dearmor -o /usr/share/keyrings/githubcli-archive-keyring.gpg;
RUN echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | tee /etc/apt/sources.list.d/github-cli.list > /dev/null;
RUN apt update && apt install -y gh;

# Uninstall old version of pandoc
# RUN sudo apt-get purge pandoc pandoc-citeproc pandoc-data \
# && sudo apt-get autoremove --purge

# Install pandoc
RUN wget https://github.com/jgm/pandoc/releases/download/3.2.1/pandoc-3.2.1-1-amd64.deb \
&& sudo apt-get install ./pandoc-3.2.1-1-amd64.deb

# Create new symlinks
RUN ln -s /usr/bin/pandoc /usr/lib/rstudio-server/bin/pandoc

# Add curl, bzip2, libbz2-dev, liblzma-dev
RUN apt-get update -qq && apt-get -y --no-install-recommends install \
bzip2 \
curl \
libbz2-dev \
liblzma-dev

# Install pip3 and installation tools
RUN apt-get -y --no-install-recommends install \
python3-pip python3-dev

# DaSEH package
RUN Rscript -e "options(warn = 2); install.packages('remotes'); remotes::install_github('fhdsl/dasehr'); remotes::install_github('MatthewBJane/ThemePark')"

# R packages
RUN Rscript -e "options(warn = 2);install.packages( \
c('bookdown', \
'here', \
'kableExtra', \
'naniar', \
'pander'), \
repos = 'https://cloud.r-project.org/')"

# Other packages
RUN Rscript -e "devtools::install_github('hadley/emo')"
RUN Rscript -e "install.packages('esquisse')"
RUN Rscript -e "install.packages('directlabels')"
RUN Rscript -e "install.packages('plotly')"
RUN Rscript -e "install.packages('tidylog')"
RUN Rscript -e "install.packages('patchwork')"
RUN Rscript -e "install.packages('corrplot')"
RUN Rscript -e "install.packages('broom')"
RUN Rscript -e "install.packages('config')"
RUN Rscript -e "install.packages('optparse')"
RUN Rscript -e "install.packages('faraway')"
RUN Rscript -e "install.packages('epitools')"

# Install pdflatex
RUN apt-get install -y texlive-latex-base texlive-latex-extra
RUN apt-get install -y texlive-fonts-recommended texlive-latex-recommended
RUN Rscript -e "options(warn = 2); remotes::install_github('fhdsl/dasehr')"

# Copy over git token
COPY git_token.txt .

# Set final workdir for commands
WORKDIR /home/rstudio
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