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1 Commits
Author | SHA1 | Date |
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Andrea Dell'Amico | 86dd7cf0bf |
15
Dockerfile
15
Dockerfile
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@ -6,8 +6,13 @@ LABEL org.d4science.image.licenses="EUPL-1.2" \
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org.d4science.image.authors="Andrea Dell'Amico <andrea.dellamico@isti.cnr.it>"
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org.d4science.image.authors="Andrea Dell'Amico <andrea.dellamico@isti.cnr.it>"
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ENV DEBIAN_FRONTEND noninteractive
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ENV DEBIAN_FRONTEND noninteractive
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# Some R dependencies
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# Upgrade, install some R dependencies and base python3
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RUN apt-get update && apt-get install -y \
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RUN apt-get update --yes && \
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apt-get dist-upgrade --yes && \
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apt-get install --yes --no-install-recommends \
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python3 \
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python3-pip \
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curl \
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jags \
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jags \
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libxml2 \
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libxml2 \
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git \
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git \
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@ -16,6 +21,8 @@ RUN apt-get update && apt-get install -y \
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libsodium-dev \
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libsodium-dev \
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libudunits2-dev \
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libudunits2-dev \
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libfontconfig1-dev \
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libfontconfig1-dev \
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librdf0 \
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librdf0-dev \
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netcdf-bin \
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netcdf-bin \
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libcairo2-dev \
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libcairo2-dev \
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libharfbuzz-dev \
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libharfbuzz-dev \
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@ -57,8 +64,7 @@ RUN for cr in `cat /tmp/jupyter-image-r-cran-pkgs.txt` ; do \
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# From github
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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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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=$GITHUB_PAT" >> /usr/local/lib/R/etc/Renviron.site
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RUN echo "GITHUB_PAT=$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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#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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# Rscript --slave --no-site-file --no-init-file --no-save --no-restore-history \
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# -e " require(devtools); devtools::install_github('$g')" ; done
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# -e " require(devtools); devtools::install_github('$g')" ; done
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@ -69,6 +75,7 @@ RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/_
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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 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 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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RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest tokami/lbmsmt
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RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest james-thorson/FishLife
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# Ensure that we remove the source packages
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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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RUN rm -fr /tmp/downloaded_packages/*
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