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add ingest merfish ci #229

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Mar 14, 2024
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remove unnecessary condaenv cmd
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SarahOuologuem committed Mar 14, 2024

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commit cae7a9f548d5bc889472fce88a4f5b3dfadd7734
1 change: 0 additions & 1 deletion .github/workflows/spatial_deconvolution-ci.yml
Original file line number Diff line number Diff line change
@@ -78,7 +78,6 @@ jobs:
- name: Replace template contents in configuration file
run: |
cd deconvolution
sed -i 's+condaenv:+conda_env: pipeline_env+g' pipeline.yml
sed -i 's+use_gpu:+use_gpu: False+g' pipeline.yml
sed -i 's+max_epochs: 400+max_epochs: 50+g' pipeline.yml

5 changes: 0 additions & 5 deletions .github/workflows/spatial_ingestion_merfish-ci.yml
Original file line number Diff line number Diff line change
@@ -82,11 +82,6 @@ jobs:
cd spatial/ingestion_merfish
curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/main/docs/ingesting_merfish_data/pipeline.yml

- name: Replace template contents in configuration file
run: |
cd spatial/ingestion_merfish
sed -i 's+condaenv:+conda_env: pipeline_env+g' pipeline.yml

- name: File tree
if: env.debug == 'true'
run: tree spatial/ingestion_merfish
5 changes: 0 additions & 5 deletions .github/workflows/spatial_ingestion_visium-ci.yml
Original file line number Diff line number Diff line change
@@ -85,11 +85,6 @@ jobs:
cd spatial/ingestion
curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/main/docs/ingesting_visium_data/pipeline.yml

- name: Replace template contents in configuration file
run: |
cd spatial/ingestion
sed -i 's+condaenv:+conda_env: pipeline_env+g' pipeline.yml

- name: File tree
if: env.debug == 'true'
run: tree spatial/ingestion