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Dockerfile
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FROM rocker/verse:4.0.1
# system dependencies
RUN export DEBIAN_FRONTEND=noninteractive; apt-get -y update \
&& apt-get install -y gdal-bin=3.0.4+dfsg-1build3 \
libgdal-dev=3.0.4+dfsg-1build3 \
libgeos-dev=3.8.0-1build1 \
libgeos++-dev=3.8.0-1build1 \
libudunits2-dev=2.2.26-5 \
make=4.2.1-1.2 \
pandoc=2.5-3build2 \
pandoc-citeproc=0.15.0.1-1build4
# working directory name
WORKDIR /home/rstudio/hkl-mirs
# install renv R package
ENV RENV_VERSION 0.11.0-6
RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cran.r-project.org'))"
RUN R -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"
# Restore renv cache
COPY renv.lock renv.lock
RUN chown -R rstudio . \
&& sudo -u rstudio Rscript -e 'renv::consent(provided = TRUE)' \
&& sudo -u rstudio Rscript -e 'Sys.setenv(R_INSTALL_STAGED = FALSE)' \
&& sudo -u rstudio R -e 'renv::restore(repos = c(RSPM = "https://packagemanager.rstudio.com/all/latest", CRAN = "https://cran.r-project.org/"))'
# install compendium
RUN sudo -u rstudio Rscript -e 'remotes::install_github("henningte/hklmirs")'
# labels
LABEL maintainer = "Henning Teickner <henning.teickner@uni-muenster.de>" \
org.opencontainers.image.authors = "Henning Teickner <henning.teickner@uni-muenster.de>" \
author.orcid = "0000-0002-3993-1182" \
org.opencontainers.image.version = "0.3.0" \
org.opencontainers.image.licenses = "GPL-3"
# instructions
# to build the image, navigate to the directory with the Dockerfile and run (the image has a size of ~7 Gb):
# docker build -t hklmirs:0.3.0 .
# to run the image in a container, do:
# docker run --rm -e PASSWORD=hkl -p 8787:8787 -v $(pwd):/home/rstudio hklmirs:0.3.0
# to reproduce the analyses, run (takes about 12 h and occupies additional 2 Gb disk space)
# docker run --rm -v $(pwd):/home/rstudio hklmirs:0.3.0 R -e 'setwd("/home/rstudio/hkl-mirs"); rmarkdown::render("analysis/paper/001-paper-main.Rmd");'