Threads documentation #149
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| name: Run tutorials (refmap) | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| env: | |
| debug: 'true' | |
| jobs: | |
| refmap: | |
| 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 '.[refmap_old]' | |
| 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 | |
| # Note: all three files are renamed during the download to trim the "subsample_" prefix | |
| - name: Preparing the data | |
| run: | | |
| mkdir -p reference_mapping && cd reference_mapping | |
| mkdir data.dir && cd data.dir | |
| curl -L -o pancreas_querydata.h5ad https://figshare.com/ndownloader/files/43166068 | |
| curl -L -o pancreas_refdata.h5mu https://figshare.com/ndownloader/files/43166074 | |
| cd .. | |
| mkdir -p models && cd models | |
| mkdir -p pancreas_model | |
| mkdir -p pancreas_model_scanvi | |
| curl -L -o pancreas_model_scanvi/model.pt https://figshare.com/ndownloader/files/43166410 | |
| curl -L -o pancreas_model/model.pt https://figshare.com/ndownloader/files/43166413 | |
| - name: Preparing the configuration file | |
| shell: bash -el {0} | |
| run: | | |
| cd reference_mapping | |
| panpipes refmap config | |
| - name: Edit the submission file | |
| run: | | |
| cd reference_mapping | |
| curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/main/docs/refmap_pancreas/pipeline.yml | |
| #scib is not up to date with scanpy | |
| - name: Replace template contents in configuration file | |
| run: | | |
| cd reference_mapping | |
| sed -i 's+/Users/fabiola.curion/Documents/devel/miniconda3/envs/pipeline_env+pipeline_env+g' pipeline.yml | |
| sed -i 's+/Users/fabiola.curion/Documents/devel/data_test.dir/data_for_scvi_test/pancreas_model/model.pt+models/pancreas_model/model.pt+g' pipeline.yml | |
| sed -i 's+/Users/fabiola.curion/Documents/devel/data_test.dir/data_for_scvi_test/pancreas_model_scanvi/model.pt+models/pancreas_model_scanvi/model.pt+g' pipeline.yml | |
| sed -i 's+max_epochs: 200+max_epochs: 20+g' pipeline.yml | |
| sed -i 's+run: True+run: False+g' pipeline.yml | |
| - name: File tree | |
| if: env.debug == 'true' | |
| run: tree reference_mapping | |
| - name: Review pipeline tasks | |
| shell: bash -el {0} | |
| run: | | |
| cd reference_mapping | |
| panpipes refmap show full --local | |
| - name: Run pipeline tasks | |
| shell: bash -el {0} | |
| run: | | |
| cd reference_mapping | |
| panpipes refmap make full --local | |
| - name: File tree | |
| if: env.debug == 'true' | |
| run: tree reference_mapping |