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fisheriesa
Author | SHA1 | Date |
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Andrea Dell'Amico | 0c69efe541 | |
Andrea Dell'Amico | 161ad3c92f | |
Andrea Dell'Amico | 0e724221fa | |
Andrea Dell'Amico | 236cbd8eed | |
Andrea Dell'Amico | 48a8d77f96 | |
Andrea Dell'Amico | c072e3324c | |
Andrea Dell'Amico | 50c72f5fe1 | |
Andrea Dell'Amico | 5843c8d994 | |
Andrea Dell'Amico | 720381f977 | |
Andrea Dell'Amico | d3886c4fa9 | |
Andrea Dell'Amico | 33797272d0 | |
Andrea Dell'Amico | a33937e7a6 | |
Andrea Dell'Amico | ad0c0fd531 | |
Andrea Dell'Amico | 80cce0fc4c | |
Andrea Dell'Amico | cc8755fb10 | |
Andrea Dell'Amico | dcbb04cc78 | |
Andrea Dell'Amico | cfbda33b4c |
62
Dockerfile
62
Dockerfile
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@ -5,7 +5,69 @@ LABEL org.d4science.image.licenses="EUPL-1.2" \
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org.d4science.image.vendor="D4Science <https://www.d4science.org>" \
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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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org.d4science.image.authors="Andrea Dell'Amico <andrea.dellamico@isti.cnr.it>"
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# R required by vlab5 VRE https://support.d4science.org/issues/23536
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ENV DEBIAN_FRONTEND noninteractive
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# Upgrade, install some R dependencies and base python3
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# Add libcurl4-gnutls-dev and remove libcurl4-openssl-dev because
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#
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# libraptor2-dev : Depends: libcurl4-gnutls-dev but it is not installable
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RUN apt-get update --yes && \
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apt-get install --yes --no-install-recommends \
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libgdal-dev \
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pandoc \
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pandoc-citeproc \
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texlive-xetex \
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texlive-latex-base \
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texlive-latex-recommended \
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texlive-fonts-recommended \
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texlive-fonts-extra \
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texlive-formats-extra \
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libssl-dev \
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libxml2-dev \
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libv8-dev \
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libsecret-1-dev \
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librdf0-dev \
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libgit2-dev \
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libxslt-dev \
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librdf0 \
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redland-utils \
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rasqal-utils \
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raptor2-utils \
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libcairo2-dev \
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libpoppler-cpp-dev \
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libmagick++-dev \
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cmake \
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cargo \
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libavfilter-dev \
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libjq-dev \
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libprotobuf-dev \
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protobuf-compiler \
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libproj-dev \
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libcurl4-gnutls-dev \
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libsodium-dev \
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libudunits2-dev \
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libglpk40
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RUN mkdir -p /opt/workspace-lib
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RUN mkdir /var/log/workspace-lib
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ADD https://maven.d4science.org/nexus/content/repositories/gcube-snapshots/org/gcube/data-access/sh-fuse-integration/2.0.0-SNAPSHOT/sh-fuse-integration-2.0.0-20211005.090627-1-jar-with-dependencies.jar /opt/workspace-lib/fuse-workspace.jar
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RUN chmod 0644 /opt/workspace-lib/fuse-workspace.jar
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COPY install2r-packages.txt /rocker_scripts
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RUN for f in `cat /rocker_scripts/install2r-packages.txt` ; do install2.r --error --skipinstalled --ncpus -1 $f || exit 1 ; done
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RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/jammy/latest r-geoflow/geoflow
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RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/jammy/latest hrbrmstr/streamgraph
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# Rstudio settings
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COPY rsession.conf /etc/rstudio/rsession.conf
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COPY rsession.conf /etc/rstudio/rsession.conf
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RUN chmod 0644 /etc/rstudio/rsession.conf
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RUN chmod 0644 /etc/rstudio/rsession.conf
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RUN curl -o "${R_HOME}/etc/Rprofile.site" "https://code-repo.d4science.org/gCubeSystem/rstudio-rprofile/raw/branch/master/jupyter-Rprofile.site"
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RUN curl -o "${R_HOME}/etc/Rprofile.site" "https://code-repo.d4science.org/gCubeSystem/rstudio-rprofile/raw/branch/master/jupyter-Rprofile.site"
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RUN rm -fr /tmp/downloaded_packages/*
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RUN rm -fr /tmp/downloaded_packages/* && \
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apt-get clean && rm -rf /var/lib/apt/lists/* && \
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rm -f /tmp/R*
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@ -9,15 +9,17 @@ pipeline {
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label 'docker'
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label 'docker'
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}
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}
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environment {
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environment {
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imagename = "d4science/rstudio-d4science"
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imagename = "rstudio/rstudio-fisheriesatlas-vlab5"
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registryCredential = 'e348bfab-5580-4db6-b0e0-d854966bde08'
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hubname = "hub.dev.d4science.org"
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registryUrl = "https://hub.dev.d4science.org"
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registryCredential = 'cccd3cf5-9d6c-4044-85d6-59bede0c43f4'
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dockerImage = ''
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dockerImage = ''
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git_url='https://code-repo.d4science.org/gCubeSystem/rstudio-d4science.git'
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git_url='https://code-repo.d4science.org/gCubeSystem/rstudio-d4science.git'
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}
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}
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stages {
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stages {
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// stage('Cloning Git') {
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// stage('Cloning Git') {
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// steps {
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// steps {
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// git([url: git_url, branch: '2023-03-R4-2', credentialsId: '88b54962-1c0e-49cb-8155-22276860f346'])
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// git([url: git_url, branch: 'fisheriesatlas-vlab5', credentialsId: '88b54962-1c0e-49cb-8155-22276860f346'])
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// }
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// }
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// }
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// }
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stage('Building image') {
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stage('Building image') {
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@ -30,17 +32,17 @@ pipeline {
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stage('Deploy Image') {
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stage('Deploy Image') {
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steps{
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steps{
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script {
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script {
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docker.withRegistry( '', registryCredential ) {
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docker.withRegistry( registryUrl, registryCredential ) {
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dockerImage.push("$BUILD_NUMBER")
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dockerImage.push("$BUILD_NUMBER")
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dockerImage.push('2023-03-R4-2')
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dockerImage.push('latest')
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}
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}
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}
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}
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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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stage('Remove Unused docker image') {
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steps{
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steps{
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sh "docker rmi $imagename:$BUILD_NUMBER"
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sh "docker rmi $hubname/$imagename:$BUILD_NUMBER"
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sh "docker rmi $imagename:2023-03-R4-2"
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sh "docker rmi $hubname/$imagename:latest"
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}
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}
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}
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}
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@ -1,6 +1,6 @@
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# rstudio-d4science
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# rstudio-d4science
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Rstudio image that builds from "r-full"
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Rstudio image that builds from "d4science/rstudio-base:2023-03-R4-2"
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This is the version customized for vfisheriesatlas-vlab5, see https://support.d4science.org/issues/23536
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One branch for each corresponding *major.minor* `R` version and for each
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customization on top of the R version.
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@ -0,0 +1,20 @@
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remotes
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dotenv
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here
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magick
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pbdZMQ
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nloptr
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tinytex
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rpostgis
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gargle
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googledrive
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gsheet
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renv
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shinyWidgets
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leaflet
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leaflet.extras
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leaflet.minicharts
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leafpm
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mapedit
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xml2
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pals
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