Add notebook which integrates metag, metap, metab data #158
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| name: Execute R notebooks | |
| on: | |
| pull_request: | |
| workflow_dispatch: | |
| # run once a week | |
| schedule: | |
| - cron: "0 0 * * 0" | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - id: checkout | |
| uses: actions/checkout@v3 | |
| - id: python-setup | |
| name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.11' | |
| - id: install-juptyer | |
| name: Install Juptyer | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install jupyter | |
| - id: r-setup | |
| name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: dependencies on Linux | |
| if: runner.os == 'Linux' | |
| run: sudo apt-get install -y make libicu-dev libxml2-dev libssl-dev pandoc librdf0-dev libnode-dev libcurl4-gnutls-dev | |
| - id: r-dependencies | |
| name: Install r dependencies | |
| run: | | |
| R -e 'install.packages("renv")' | |
| R -e 'renv::restore()' | |
| R -e 'install.packages("IRkernel")' | |
| R -e 'IRkernel::installspec()' | |
| - id: execute-integration | |
| name: Execute integration notebook | |
| run: | | |
| jupyter nbconvert --execute --to notebook --inplace omics_types_integration/R/integration_notebook.ipynb | |
| - id: execute-bioscales | |
| name: Execute bioscales notebook | |
| run: | | |
| jupyter nbconvert --execute --to notebook --inplace bioscales_biogeochemical_metadata/R/bioscales_metadata.ipynb | |
| - id: execute-neon | |
| name: Execute NEON metadata notebook | |
| run: | | |
| jupyter nbconvert --execute --to notebook --inplace NEON_soil_metadata/R/NEON_data_exploration.ipynb | |
| - id: execute-taxonomic | |
| name: Execute taxonomic metadata notebook | |
| run: | | |
| jupyter nbconvert --execute --to notebook --inplace taxonomic_dist_by_soil_layer/R/taxonomic_dist_soil_layer_R.ipynb | |
| - id: execute-nom | |
| name: Execute NOM notebook | |
| run: | | |
| jupyter nbconvert --execute --to notebook --inplace NOM_visualizations/R/NOM_R_notebook.ipynb |