Add Docker and Jenkins files.
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FROM rocker/r-ver:4.2.3
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LABEL org.d4science.image.licenses="EUPL-1.2" \
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org.d4science.image.source="https://code-repo.d4science.org/gCubeSystem/r-full-4.2" \
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org.d4science.image.vendor="D4Science <https://www.d4science.org>" \
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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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# 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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fuse \
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zip \
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jq \
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openjdk-8-jdk-headless
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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('$mirror/'));" ; done
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# Install some CRAN packages from source
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ADD https://code-repo.d4science.org/gCubeSystem/r-packages-list/raw/branch/master/jupyter-image-r-cran-pkgs.txt /tmp
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RUN for cr in `cat /tmp/r_non_cran_pkgs.txt` ; do \
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pkg='$cr' ; \
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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/'));" ; done
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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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RUN apt-get clean && rm -rf /var/lib/apt/lists/* && \
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rm -f /tmp/R* /tmp/install2r-packages.txt /tmp/r_github_pkgs.txt /tmp/jupyter-image-r-cran-pkgs.txt /tmp/r_non_cran_pkgs.txt && \
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echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
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locale-gen
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@ -0,0 +1,49 @@
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// REMEMBER TO FILL THE environment section with your values.
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// the following filed should be filled: imagename, git_url
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// REMEMBER to put your Dockerfile in the root folder of your project
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// The related jenkinsjob template is here:
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pipeline {
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agent {
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label 'docker'
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}
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environment {
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imagename = "d4science/r-full" //TO FILL WITH THE RIGHT VALUE (RepositoryName) e.g. d4science/RepositoryName
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registryCredential = 'e348bfab-5580-4db6-b0e0-d854966bde08'
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dockerImage = ''
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git_url='https://code-repo.d4science.org/gCubeSystem/r-full-4.2.git' // SET HERE THE URL OF YOUR NEW GIT PROJECT
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}
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stages {
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stage('Cloning Git') {
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steps {
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git([url: git_url, branch: 'main', credentialsId: '88b54962-1c0e-49cb-8155-22276860f346'])
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}
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}
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stage('Building image') {
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steps{
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script {
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dockerImage = docker.build imagename
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}
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}
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}
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stage('Deploy Image') {
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steps{
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script {
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docker.withRegistry( '', registryCredential ) {
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dockerImage.push("$BUILD_NUMBER")
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dockerImage.push('4.2')
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}
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}
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}
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}
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stage('Remove Unused docker image') {
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steps{
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sh "docker rmi $imagename:$BUILD_NUMBER"
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sh "docker rmi $imagename:4.2"
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}
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}
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}
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}
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