Branch for the fisheriatlas-vlab5 rstudio
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@ -5,17 +5,59 @@ 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 and python3 packages required by wb3 ecosystem https://support.d4science.org/issues/26459
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# R required by vlab5 VRE https://support.d4science.org/issues/23536
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COPY wb3-install2r-packages.txt /rocker_scripts
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RUN for f in `cat //rocker_scripts/wb3-install2r-packages.txt` ; do install2.r --error --skipinstalled --ncpus -1 $f || exit 1 ; done
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RUN pip3 install \
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ENV DEBIAN_FRONTEND noninteractive
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numpy \
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# Upgrade, install some R dependencies and base python3
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mbtr \
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RUN apt-get update --yes && \
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pandas
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apt-get dist-upgrade --yes && \
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apt-get install --yes --no-install-recommends \
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libgdal-devel \
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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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libcurl4-openssl-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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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 $f || exit 1 ; done
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RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/jammy/latest r-geoflow/geoflow
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RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/jammy/latest hrbrmstr/streamgraph
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# Rstudio settings
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# Rstudio settings
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COPY rsession.conf /etc/rstudio/rsession.conf
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COPY rsession.conf /etc/rstudio/rsession.conf
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RUN chmod 0644 /etc/rstudio/rsession.conf
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RUN chmod 0644 /etc/rstudio/rsession.conf
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RUN curl -o "${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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@ -9,7 +9,7 @@ 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 = "rstudio/rstudio-wb3-ecosystem"
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imagename = "rstudio/rstudio-fisheriesatlas-vlab5"
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hubname = "hub.dev.d4science.org"
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hubname = "hub.dev.d4science.org"
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registryUrl = "https://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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registryCredential = 'cccd3cf5-9d6c-4044-85d6-59bede0c43f4'
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@ -19,7 +19,7 @@ pipeline {
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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: 'wb3-ecosystem', 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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@ -2,5 +2,5 @@
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Rstudio image that builds from "d4science/rstudio-base:2023-03-R4-2"
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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 WB3 ecosystem, see https://support.d4science.org/issues/26459
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This is the version customized for vfisheriesatlas-vlab5, see https://support.d4science.org/issues/23536
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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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@ -1,28 +0,0 @@
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abind
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caret
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corrplot
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devtools
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dendextend
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ncdf4
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parallel
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pdftools
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rgbif
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reticulate
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tidyverse
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tidymodels
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raster
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DALEX
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DALEXtra
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xgboost
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RSQLite
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feather
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vroom
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virtualspecies
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usdm
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robis
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RColorBrewer
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fields
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pastecs
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ecospat
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mvrsquared
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bestNormalize
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