OpenMS/.github/workflows/knime_tests.yml at develop · mwalzer/OpenMS · GitHub

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name: 'Test KNIME workflows'
on:
  workflow_dispatch:
    inputs:
      updateURL:
        type: string
        description: use a specific location for the knime update site
        default: https://abibuilder.cs.uni-tuebingen.de/archive/openms/knime-plugin/updateSite/nightly/
jobs:
  test-knime:
    env:
      GH_TOKEN: ${{ github.token }}
      KNIME_MAJOR_VERSION: 5
      KNIME_MINOR_VERSION: 3
      INSTALLATION_DIR: ${{ github.workspace }}
    runs-on: ubuntu-latest
    steps:
      - name: Set more env
        run: |
          echo "KNIME_VERSION=${KNIME_MAJOR_VERSION}.${KNIME_MINOR_VERSION}" >> $GITHUB_ENV
          echo "KNIME_DIR=${INSTALLATION_DIR}/knime" >> $GITHUB_ENV
          echo "DOWNLOAD_URL=https://download.knime.org/analytics-platform/linux/knime-latest${KNIME_MAJOR_VERSION}${KNIME_MINOR_VERSION}-linux.gtk.x86_64.tar.gz" >> $GITHUB_ENV

      - name: Install deps
        run: |
          apt-get install -y software-properties-common curl tzdata libgtk2.0-0 libxtst6 \
            && apt-get install -y libwebkitgtk-3.0-0 python python-dev python-pip curl \
            && apt-get install -y r-base r-recommended
          pip install pandas protobuf

      - name: Install KNIME
        run: |
          curl -L "$DOWNLOAD_URL" | tar vxz -C $INSTALLATION_DIR \
            && mv $INSTALLATION_DIR/knime_* $INSTALLATION_DIR/knime

      - name: Install and start Rserve
        run: |
          mkdir -p ~/local/R_libs
          R -e 'install.packages(c("Rserve"), repos="http://cran.rstudio.com/", lib="~/local/R_libs/")'

      - name: Install OpenMS plugin
        run: |
          "$KNIME_DIR/knime" -application org.eclipse.equinox.p2.director \
            -r "http://update.knime.com/analytics-platform/${KNIME_VERSION},${{ inputs.updateURL }}" \
            -p2.arch x86_64 \
            -profileProperties org.eclipse.update.install.features=true \
            -i "de.openms.feature.feature.group,com.genericworkflownodes.knime.feature.feature.group,de.openms.thirdparty.feature.feature.group" \
            -p KNIMEProfile \
            -nosplash

      - name: Install other plugins
        run: |
          "$KNIME_DIR/knime" -application org.eclipse.equinox.p2.director \
            -r "http://update.knime.com/analytics-platform/${KNIME_VERSION},http://update.knime.com/community-contributions/trunk" \
            -p2.arch x86_64 \
            -profileProperties org.eclipse.update.install.features=true \
            -i "org.knime.features.r.feature.group,org.knime.features.chem.types.feature.group,org.rdkit.knime.feature.feature.group,org.knime.features.ext.svg.feature.group" \
            -p KNIMEProfile \
            -nosplash

      - name: Create Workspace and fill with input data
        run: |
          wget -c https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Example_Data.tar.gz -O - | tar -xz

      - name:  Clone Tutorials
        run: |
          gh repo clone OpenMS/Tutorials
          pushd Tutorials/Workflows
            ./executeBatch.sh "$KNIME_DIR/knime" ${INSTALLATION_DIR}
            cat log*.txt
          popd