69 lines
2.9 KiB
Docker
69 lines
2.9 KiB
Docker
FROM rocker/r-ver:4.1.3
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LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
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org.opencontainers.image.source="https://github.com/rocker-org/rocker-versioned2" \
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org.opencontainers.image.vendor="Rocker Project" \
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org.opencontainers.image.authors="Carl Boettiger <cboettig@ropensci.org>"
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# Some R dependencies
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RUN apt-get update && apt-get install -y \
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jags \
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libxml2 \
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git \
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gdal-bin \
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libgdal-dev \
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libsodium-dev \
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libudunits2-dev \
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libfontconfig1-dev \
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netcdf-bin \
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libcairo2-dev \
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libharfbuzz-dev \
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libfribidi-dev \
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sshpass \
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p7zip-full \
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sox \
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imagemagick \
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proj-bin \
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proj-data \
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libgsl23 \
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postgresql-server-dev-all \
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libsecret-1-0
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# Install the R packages we need, using the binary distribution
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# at https://packagemanager.rstudio.com/client/#/repos/1/overview
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ADD https://code-repo.d4science.org/gCubeSystem/r-packages-list/raw/branch/master/install2r-packages.txt /tmp
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RUN for f in `cat /tmp/install2r-packages.txt` ; do install2.r --error --skipinstalled --ncpus -1 $f ; done
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# Non CRAN repositories
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ADD https://code-repo.d4science.org/gCubeSystem/r-packages-list/raw/branch/master/r_non_cran_pkgs.txt /tmp
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RUN for l in `cat /tmp/r_non_cran_pkgs.txt` ; do \
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pkg=`echo $l | cut -d : -f 1` ; \
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mirror=`echo $l | cut -d : -f 2-` ; \
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Rscript --slave --no-site-file --no-init-file --no-save --no-restore-history \
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-e "install.packages(pkgs='$pkg', repos=c('$mirror/'));" ; done
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# Install TMB from sources
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RUN pkg='TMB' ; \
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mirror='https://cloud.r-project.org' ; \
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Rscript --slave --no-site-file --no-init-file --no-save --no-restore-history \
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-e "install.packages(pkgs='$pkg', repos=c('$mirror/'));"
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# From github
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ADD https://code-repo.d4science.org/gCubeSystem/r-packages-list/raw/branch/master/r_github_pkgs.txt /tmp
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RUN mkdir -p /etc/R
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RUN echo "GITHUB_PAT=$GITHUB_PAT" >> /etc/R/Renviron.site
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#RUN for g in `cat /tmp/r_github_pkgs.txt` ; do \
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# Rscript --slave --no-site-file --no-init-file --no-save --no-restore-history \
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# -e " require(devtools); devtools::install_github('$g')" ; done
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#RUN for g in `cat /tmp/r_github_pkgs.txt` ; do installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest $g ; done
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#RUN grep -v "GITHUB_PATH" /etc/R/Renviron.site > /etc/R/Renviron.site.1
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#RUN mv -f /etc/R/Renviron.site.1 /etc/R/Renviron.site
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RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest DanOvando/sraplus
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RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest sofia-tsaf/SOFIA
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RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest jabbamodel/JABBA
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RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest tokami/lbmsmt
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# Ensure that we remove the source packages
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RUN rm -fr /tmp/downloaded_packages/*
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