diff --git a/Dockerfile b/Dockerfile index c04d613..c2c8347 100644 --- a/Dockerfile +++ b/Dockerfile @@ -5,6 +5,17 @@ LABEL org.d4science.image.licenses="EUPL-1.2" \ org.d4science.image.vendor="D4Science " \ org.d4science.image.authors="Andrea Dell'Amico " +# R and python3 packages required by wb3 ecosystem https://support.d4science.org/issues/26459 +COPY wb3-install2r-packages.txt /rocker_scripts +RUN for f in `cat //rocker_scripts/wb3-install2r-packages.txt` ; do install2.r --error --skipinstalled --ncpus -1 $f || exit 1 ; done + +RUN pip3 install \ + numpy \ + mbtr \ + pandas \ + pickle + +# Rstudio settings COPY rsession.conf /etc/rstudio/rsession.conf RUN chmod 0644 /etc/rstudio/rsession.conf RUN curl -o "${R_HOME}/etc/Rprofile.site" "https://code-repo.d4science.org/gCubeSystem/rstudio-rprofile/raw/branch/master/jupyter-Rprofile.site" diff --git a/Jenkinsfile-wb3-ecosystem b/Jenkinsfile-wb3-ecosystem new file mode 100644 index 0000000..a215ae3 --- /dev/null +++ b/Jenkinsfile-wb3-ecosystem @@ -0,0 +1,65 @@ +// REMEMBER TO FILL THE environment section with your values. +// the following filed should be filled: imagename, git_url +// REMEMBER to put your Dockerfile in the root folder of your project +// The related jenkinsjob template is here: + + +pipeline { + agent { + label 'docker' + } + environment { + imagename = "hub.d4science.org/rstudio/rstudio-wb3-ecosystem" + registryUrl 'https://hub.d4science.org' + registryCredential = 'cccd3cf5-9d6c-4044-85d6-59bede0c43f4' + dockerImage = '' + git_url='https://code-repo.d4science.org/gCubeSystem/rstudio-d4science.git' + } + stages { + // stage('Cloning Git') { + // steps { + // git([url: git_url, branch: 'wb3-ecosystem', credentialsId: '88b54962-1c0e-49cb-8155-22276860f346']) + // } + // } + stage('Building image') { + steps{ + script { + dockerImage = docker.build imagename + } + } + } + stage('Deploy Image') { + steps{ + script { + docker.withRegistry( 'https://hub.d4science.org', registryCredential ) { + dockerImage.push("$BUILD_NUMBER") + dockerImage.push('wb3-ecosystem') + } + } + } + } + stage('Remove Unused docker image') { + steps{ + sh "docker rmi $imagename:$BUILD_NUMBER" + sh "docker rmi $imagename:wb3-ecosystem" + + } + } + } + // post-build actions + post { + success { + echo 'The docker pipeline worked!' + emailext to: 'jenkinsbuilds@d4science.org', + subject: "[Jenkins DockerPipeline D4S] build ${currentBuild.fullDisplayName} worked", + body: "Build time: ${currentBuild.durationString}. See ${env.BUILD_URL}" + } + failure { + echo 'The docker pipeline has failed' + emailext attachLog: true, + to: 'jenkinsbuilds@d4science.org', + subject: "[Jenkins DockerPipeline D4S] build ${currentBuild.fullDisplayName} failed for image ${imagename}", + body: "Something is wrong with ${env.BUILD_URL}" + } + } +} diff --git a/wb3-install2r-packages.txt b/wb3-install2r-packages.txt new file mode 100644 index 0000000..a06c09b --- /dev/null +++ b/wb3-install2r-packages.txt @@ -0,0 +1,28 @@ +abind +caret +corrplot +devtools +dendextend +ncdf4 +parallel +pdftools +rgbif +reticulate +tidyverse +tidymodels +raster +DALEX +DALEXtra +xgboost +RSQLite +feather +vroom +virtualspecies +usdm +robis +RColorBrewer +fields +pastecs +ecospat +mvrsquared +bestNormalize