From MuData to SpatialData #339
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Run tutorials (spatial ingest merfish) | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| env: | |
| debug: 'true' | |
| jobs: | |
| spatial_ingest_merfish: | |
| 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_merfish spatial/ingestion_merfish/data | |
| cd spatial/ingestion_merfish/data | |
| curl -L -o cell_by_gene.csv https://figshare.com/ndownloader/files/45028624 | |
| curl -L -o cell_metadata.csv https://figshare.com/ndownloader/files/45028621 | |
| mkdir images | |
| cd images | |
| curl -L -o micron_to_mosaic_pixel_transform.csv https://figshare.com/ndownloader/files/45028645 | |
| # Note: we run the following to test that the commands works | |
| - name: Preparing the configuration file | |
| shell: bash -el {0} | |
| run: | | |
| cd spatial/ingestion_merfish | |
| panpipes qc_spatial config | |
| - name: Preparing the submission file | |
| run: | | |
| cd spatial/ingestion_merfish | |
| curl -o sample_file_qc_merfish.txt https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/sarah_spatialData/docs/ingesting_merfish_data/sample_file_qc_merfish.txt | |
| - name: Preparing the yaml file | |
| run: | | |
| cd spatial/ingestion_merfish | |
| curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/sarah_spatialData/docs/ingesting_merfish_data/pipeline.yml | |
| - name: File tree | |
| if: env.debug == 'true' | |
| run: tree spatial/ingestion_merfish | |
| - name: Review pipeline tasks | |
| shell: bash -el {0} | |
| run: | | |
| cd spatial/ingestion_merfish | |
| panpipes qc_spatial show full --local | |
| - name: Run pipeline tasks | |
| shell: bash -el {0} | |
| run: | | |
| cd spatial/ingestion_merfish | |
| panpipes qc_spatial make full --local | |
| - name: File tree | |
| if: env.debug == 'true' | |
| run: tree spatial/ingestion_merfish |