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| name: Build and Push Docker Images (rocker-eiaspatial) | ||
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| on: | ||
| push: | ||
| branches: | ||
| - develop | ||
| - main | ||
| paths: | ||
| - ".github/workflows/pipeline-rocker-eiaspatial.yml" | ||
| - "rocker-eiaspatial/**" | ||
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| permissions: | ||
| contents: read | ||
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| jobs: | ||
| build_and_push_dev: | ||
| runs-on: "self-hosted" | ||
| if: startsWith(github.ref, 'refs/heads/develop') | ||
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| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v3 | ||
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| - name: Get short SHA | ||
| uses: benjlevesque/short-sha@v2.2 | ||
| id: short-sha | ||
| with: | ||
| length: 7 | ||
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| - name: Set up Docker Buildx | ||
| uses: docker/setup-buildx-action@v2 | ||
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| - name: Login to Docker Hub | ||
| uses: docker/login-action@v2 | ||
| with: | ||
| username: ${{ secrets.DOCKERHUB_USERNAME }} | ||
| password: ${{ secrets.DOCKERHUB_PASSWORD }} | ||
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| - name: Build and Push Docker Image (dev) | ||
| uses: docker/build-push-action@v4 | ||
| with: | ||
| context: ./rocker-eiaspatial | ||
| file: ./rocker-eiaspatial/Dockerfile | ||
| push: true | ||
| tags: | | ||
| ${{ secrets.DOCKERHUB_USERNAME }}/rocker-eiaspatial:dev-${{ secrets.ROCKER_EIASPATIAL_RELEASE_VERSION }}-${{ steps.short-sha.outputs.sha }} | ||
| ${{ secrets.DOCKERHUB_USERNAME }}/rocker-eiaspatial:dev-${{ secrets.ROCKER_EIASPATIAL_RELEASE_VERSION }} | ||
| cache-from: type=gha | ||
| cache-to: type=gha,mode=max | ||
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| build_and_push_prod: | ||
| runs-on: "self-hosted" | ||
| if: startsWith(github.ref, 'refs/heads/main') | ||
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| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v3 | ||
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| - name: Login to Docker Hub | ||
| uses: docker/login-action@v2 | ||
| with: | ||
| username: ${{ secrets.DOCKERHUB_USERNAME }} | ||
| password: ${{ secrets.DOCKERHUB_PASSWORD }} | ||
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| - name: Pull "dev" Docker image | ||
| run: docker pull ${{ secrets.DOCKERHUB_USERNAME }}/rocker-eiaspatial:dev-${{ secrets.ROCKER_EIASPATIAL_RELEASE_VERSION }} | ||
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| - name: Tag producion Docker image | ||
| run: docker tag ${{ secrets.DOCKERHUB_USERNAME }}/rocker-eiaspatial:dev-${{ secrets.ROCKER_EIASPATIAL_RELEASE_VERSION }} ${{ secrets.DOCKERHUB_USERNAME }}/rocker-eiaspatial:${{ secrets.ROCKER_EIASPATIAL_RELEASE_VERSION }} | ||
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| - name: Push Docker image | ||
| run: docker push ${{ secrets.DOCKERHUB_USERNAME }}/rocker-eiaspatial:${{ secrets.ROCKER_EIASPATIAL_RELEASE_VERSION }} | ||
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| - name: Tag producion Docker image (non specified version) | ||
| run: docker tag ${{ secrets.DOCKERHUB_USERNAME }}/rocker-eiaspatial:${{ secrets.ROCKER_EIASPATIAL_RELEASE_VERSION }} ${{ secrets.DOCKERHUB_USERNAME }}/rocker-eiaspatial | ||
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| - name: Push Docker image (non specified version) | ||
| run: docker push ${{ secrets.DOCKERHUB_USERNAME }}/rocker-eiaspatial |
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| # docker build -t rocker440 --progress=plain . > >(stdbuf -oL tee docker_build_output.log) 2> >(stdbuf -oL tee -a docker_build_output.log) | ||
| # docker run --name cg -p 8787:8787 --rm -ti -e PASSWORD=1234 rocker440 | ||
| FROM rocker/rstudio:4.4.0 | ||
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| ### Providing root privillages to default "rstudio" user account | ||
| RUN sudo usermod -aG sudo rstudio | ||
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| ### OS Packages installation | ||
| RUN sudo apt-get update && sudo apt-get install aptitude gdebi-core curl wget tar build-essential cmake make default-jre default-jdk cron screen pkg-config protobuf-compiler libfontconfig1-dev libgsl-dev libudunits2-dev libprotobuf-dev libjq-dev libmagick++-dev gfortran fftw3 fftw3-dev libxml2-dev libcurl4-openssl-dev libfontconfig1-dev libssl-dev libsodium-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libgmp3-dev libmpfr-dev libarchive-dev gnupg libmysqlclient-dev -y | ||
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| ### GDAL installation | ||
| # RUN sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable # Not necessary | ||
| RUN sudo apt-get update && sudo apt-get install libgdal-dev libgeos-dev libproj-dev -y | ||
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| ### gsutil installation | ||
| RUN sudo echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.cloud.google.com/apt cloud-sdk main" | sudo tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | sudo apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - && sudo apt-get update -y && sudo apt-get install google-cloud-cli -y | ||
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| ### NCO installation | ||
| RUN sudo aptitude install nco -y | ||
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| ### CROP models installation | ||
| ## DSSAT installation | ||
| RUN sudo mkdir -p /opt/DSSAT/v4.7.5.30 && \ | ||
| sudo chown -R rstudio:users /opt/DSSAT/v4.7.5.30/. | ||
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| RUN sudo mkdir -p /opt/DSSAT/v4.8.1.40 && \ | ||
| sudo chown -R rstudio:users /opt/DSSAT/v4.8.1.40/. | ||
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| # v4.7.5.30 installation | ||
| RUN cd /opt/DSSAT/v4.7.5.30 && \ | ||
| git clone https://github.com/DSSAT/dssat-csm-os.git --depth 1 --branch v4.7.5.30 && \ | ||
| git clone https://github.com/DSSAT/dssat-csm-data.git | ||
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| RUN cd /opt/DSSAT/v4.7.5.30/dssat-csm-os && \ | ||
| mkdir build && \ | ||
| cd build && \ | ||
| cmake .. && \ | ||
| make | ||
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| # Adjusting filesystem to DSSAT compiler requirements | ||
| RUN cp /opt/DSSAT/v4.7.5.30/dssat-csm-os/build/bin/* /opt/DSSAT/v4.7.5.30 | ||
| RUN cp -r /opt/DSSAT/v4.7.5.30/dssat-csm-os/Data/. /opt/DSSAT/v4.7.5.30 | ||
| RUN cp -r /opt/DSSAT/v4.7.5.30/dssat-csm-data/* /opt/DSSAT/v4.7.5.30 | ||
| RUN sed -i 's,/usr/local,opt/DSSAT/v4.7.5.30,g' /opt/DSSAT/v4.7.5.30/DSSATPRO.L47 | ||
| RUN chown -R rstudio:rstudio /opt/DSSAT/v4.7.5.30/* | ||
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| # v4.8.1.40 installation | ||
| RUN cd /opt/DSSAT/v4.8.1.40 && \ | ||
| git clone https://github.com/DSSAT/dssat-csm-os.git --depth 1 --branch v4.8.1.40 && \ | ||
| git clone https://github.com/DSSAT/dssat-csm-data.git | ||
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| RUN cd /opt/DSSAT/v4.8.1.40/dssat-csm-os && \ | ||
| mkdir build && \ | ||
| cd build && \ | ||
| cmake .. && \ | ||
| make | ||
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| # Adjusting filesystem to DSSAT compiler requirements | ||
| RUN cp /opt/DSSAT/v4.8.1.40/dssat-csm-os/build/bin/* /opt/DSSAT/v4.8.1.40 | ||
| RUN cp -r /opt/DSSAT/v4.8.1.40/dssat-csm-os/Data/. /opt/DSSAT/v4.8.1.40 | ||
| RUN cp -r /opt/DSSAT/v4.8.1.40/dssat-csm-data/* /opt/DSSAT/v4.8.1.40 | ||
| RUN sed -i 's,/usr/local,opt/DSSAT/v4.8.1.40,g' /opt/DSSAT/v4.8.1.40/DSSATPRO.L48 | ||
| RUN chown -R rstudio:rstudio /opt/DSSAT/v4.8.1.40/* | ||
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| ## ApsimX | ||
| RUN sudo apt-get update && sudo apt-get install libsqlite3-dev dotnet-sdk-6.0 -y | ||
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| RUN cd /opt/ && \ | ||
| sudo git clone https://github.com/APSIMInitiative/ApsimX && \ | ||
| sudo chown -R rstudio:users /opt/ApsimX/. && \ | ||
| dotnet build -c Release ./ApsimX/ApsimX.sln | ||
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| ## rJava dependencies | ||
| RUN sudo R CMD javareconf | ||
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| ### R packages installation | ||
| COPY packages.R packages.R | ||
| RUN sudo Rscript packages.R | ||
| RUN rm packages.R |
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| install.packages(c('devtools', 'shapefiles', | ||
| 'ncdf4', 'terra', 'rworldmap', 'spatstat.geom', 'ggmap', 'rgee', | ||
| 'leaflet', 'dismo', 'gdalUtilities', 'Hmisc', | ||
| 'circlize', 'diagis', 'ggnewscale', 'lmerTest', 'lme4', 'metafor', | ||
| 'metan', 'pbapply', 'FactoMineR', 'doParallel', 'ggpubr', 'broom', | ||
| 'mlr3', 'RInside', 'doSNOW', 'Microsoft365R', 'googleCloudStorageR', | ||
| 'circular', 'miceadds', 'multimode', 'sfsmisc', 'rJava', 'R.utils', | ||
| 'reshape2', 'rworldxtra', 'RCurl', 'tidyverse', 'ranger', 'sodium', | ||
| 'pals', 'ggcorrplot', 'aws.s3', 'agricolae', 'xlsx', 'ecmwfr', | ||
| 'envirem', 'ranger', 'maps', 'dplyr', 'DSSAT', Ncpus = 4), | ||
| dependencies=TRUE, | ||
| repos='http://cran.rstudio.com/') | ||
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| devtools::install_github(c("CIAT-DAPA/analogues", | ||
| "SantanderMetGroup/loadeR.java", | ||
| "SantanderMetGroup/climate4R.UDG", | ||
| "SantanderMetGroup/loadeR", | ||
| "SantanderMetGroup/transformeR", | ||
| "SantanderMetGroup/visualizeR", | ||
| "SantanderMetGroup/downscaleR", | ||
| "femiguez/apsimx")) | ||
| devtools::install_github(c("SantanderMetGroup/convertR", | ||
| "SantanderMetGroup/climate4R.indices"), Ncpus = 4) | ||
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| devtools::install_github("bakaburg1/BaySREn") |