From MuData to SpatialData #6
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| name: Run tutorials (spatial ingest xenium) | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| env: | |
| debug: 'true' | |
| jobs: | |
| spatial_ingest_xenium: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] # , "macos-latest", "windows-latest" | |
| python-version: ["3.10"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: File tree | |
| if: env.debug == 'true' | |
| run: tree | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| auto-activate-base: true | |
| auto-update-conda: true | |
| channels: conda-forge | |
| channel-priority: strict | |
| activate-environment: pipeline_env | |
| environment-file: pipeline_env.yaml | |
| - name: Install Panpipes | |
| shell: bash -el {0} | |
| run: | | |
| pip install .[spatial] | |
| conda list | |
| - name: Conda info | |
| if: env.debug == 'true' | |
| shell: bash -el {0} | |
| run: conda info | |
| - name: Conda list | |
| if: env.debug == 'true' | |
| shell: pwsh | |
| run: conda list | |
| - name: Preparing the data | |
| run: | | |
| mkdir spatial spatial/ingestion_xenium spatial/ingestion_xenium/data | |
| cd spatial/ingestion_xenium/data | |
| curl -L -o experiment.xenium https://figshare.com/ndownloader/files/51244265 | |
| curl -L -o nucleus_boundaries.parquet https://figshare.com/ndownloader/files/51244286 | |
| curl -L -o cell_boundaries.parquet https://figshare.com/ndownloader/files/51244244 | |
| curl -L -o transcripts.parquet https://figshare.com/ndownloader/files/51244283 | |
| curl -L -o cell_feature_matrix.h5 https://figshare.com/ndownloader/files/51244247 | |
| curl -L -o cells.parquet https://figshare.com/ndownloader/files/51244259 | |
| curl -L -o morphology_mip.ome.tif https://figshare.com/ndownloader/files/51244415 | |
| curl -L -o cells.zarr.zip https://figshare.com/ndownloader/files/51244262 | |
| mkdir morphology_focus | |
| cd morphology_focus | |
| curl -L -o morphology_focus_0000.ome.tif https://figshare.com/ndownloader/files/51244277 | |
| # Note: we run the following to test that the commands works | |
| - name: Preparing the configuration file | |
| shell: bash -el {0} | |
| run: | | |
| cd spatial/ingestion_xenium | |
| panpipes qc_spatial config | |
| - name: Preparing the submission file | |
| run: | | |
| cd spatial/ingestion_xenium | |
| curl -o sample_file_qc_xenium.txt https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/sarah_spatialData/docs/ingesting_xenium_data/sample_file_qc_xenium.txt | |
| - name: Preparing the yaml file | |
| run: | | |
| cd spatial/ingestion_xenium | |
| curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/sarah_spatialData/docs/ingesting_xenium_data/pipeline.yml | |
| - name: File tree | |
| if: env.debug == 'true' | |
| run: tree spatial/ingestion_xenium | |
| - name: Review pipeline tasks | |
| shell: bash -el {0} | |
| run: | | |
| cd spatial/ingestion_xenium | |
| panpipes qc_spatial show full --local | |
| - name: Run pipeline tasks | |
| shell: bash -el {0} | |
| run: | | |
| cd spatial/ingestion_xenium | |
| panpipes qc_spatial make full --local | |
| - name: File tree | |
| if: env.debug == 'true' | |
| run: tree spatial/ingestion_xenium |