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spatial_preprocess-ci.yml
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name: Run tutorials (spatial preprocessing)
on:
push:
branches:
- main
pull_request:
branches:
- main
env:
debug: 'true'
jobs:
spatial_preprocessing:
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
# Note: we run the following to test that the commands works
- name: Preparing the configuration file
shell: bash -el {0}
run: |
mkdir spatial/preprocess
cd spatial/preprocess
panpipes preprocess_spatial config
- name: Edit the submission file
run: |
cd spatial/preprocess
curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/main/docs/preprocess_spatial_data/pipeline.yml
- name: File tree
if: env.debug == 'true'
run: tree spatial/preprocess
- name: Review pipeline tasks
shell: bash -el {0}
run: |
cd spatial/preprocess
panpipes preprocess_spatial show full --local
- name: Run pipeline tasks
shell: bash -el {0}
run: |
cd spatial/preprocess
panpipes preprocess_spatial make full --local
- name: File tree
if: env.debug == 'true'
run: tree spatial/preprocess