From MuData to SpatialData #365
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name: Run tutorials (spatial ingest visium) | |
on: | |
push: | |
branches: | |
- main | |
pull_request: | |
branches: | |
- main | |
env: | |
debug: 'true' | |
jobs: | |
spatial_ingest_visium: | |
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 spatial/ingestion/data | |
cd spatial/ingestion/data | |
mkdir V1_Human_Heart V1_Human_Lymph_Node | |
cd V1_Human_Heart | |
curl -O https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Human_Heart/V1_Human_Heart_filtered_feature_bc_matrix.h5 | |
curl -O https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Human_Heart/V1_Human_Heart_spatial.tar.gz | |
tar -xf V1_Human_Heart_spatial.tar.gz | |
cd ../V1_Human_Lymph_Node | |
curl -O https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Human_Lymph_Node/V1_Human_Lymph_Node_filtered_feature_bc_matrix.h5 | |
curl -O https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Human_Lymph_Node/V1_Human_Lymph_Node_spatial.tar.gz | |
tar -xf V1_Human_Lymph_Node_spatial.tar.gz | |
# Note: we run the following to test that the commands works | |
- name: Preparing the configuration file | |
shell: bash -el {0} | |
run: | | |
cd spatial/ingestion | |
panpipes qc_spatial config | |
- name: Preparing the submission file | |
run: | | |
cd spatial/ingestion | |
curl -o sample_file_qc_visium.txt https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/sarah_spatialData/docs/ingesting_visium_data/sample_file_qc_visium.txt | |
- name: Preparing the yaml file | |
run: | | |
cd spatial/ingestion | |
curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/sarah_spatialData/docs/ingesting_visium_data/pipeline.yml | |
- name: File tree | |
if: env.debug == 'true' | |
run: tree spatial/ingestion | |
- name: Review pipeline tasks | |
shell: bash -el {0} | |
run: | | |
cd spatial/ingestion | |
panpipes qc_spatial show full --local | |
- name: Run pipeline tasks | |
shell: bash -el {0} | |
run: | | |
cd spatial/ingestion | |
panpipes qc_spatial make full --local | |
- name: File tree | |
if: env.debug == 'true' | |
run: tree spatial/ingestion |