Update docker and pipelines

hubmapconsortium · Aug 21, 2023 · b74993e · b74993e
1 parent d362578
commit b74993e
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Showing 10 changed files with 20 additions and 10 deletions.
diff --git a/containers/azimuth/Dockerfile b/containers/azimuth/Dockerfile
@@ -5,4 +5,4 @@ RUN pip install -r requirements-freeze.txt
 
 COPY context/* .
 
-ENTRYPOINT ["python3", "/main.py"]
+CMD ["python3", "/main.py"]
diff --git a/containers/azimuth/pipeline.cwl b/containers/azimuth/pipeline.cwl
@@ -9,7 +9,9 @@ requirements:
     types:
       - $import: ./options.yml
 
-baseCommand: python3 /main.py
+baseCommand: python3
+arguments:
+  - /main.py
 
 inputs:
   matrix:

diff --git a/containers/celltypist/Dockerfile b/containers/celltypist/Dockerfile
@@ -8,4 +8,4 @@ RUN python -c "import celltypist; celltypist.models.download_models()"
 
 COPY context/* .
 
-ENTRYPOINT ["python", "/main.py"]
+CMD ["python", "/main.py"]
diff --git a/containers/celltypist/pipeline.cwl b/containers/celltypist/pipeline.cwl
@@ -9,7 +9,9 @@ requirements:
     types:
       - $import: ./options.yml
 
-baseCommand: python /main.py
+baseCommand: python
+arguments:
+  - /main.py
 
 inputs:
   matrix:

diff --git a/containers/extract-summary/Dockerfile b/containers/extract-summary/Dockerfile
@@ -5,4 +5,4 @@ RUN pip install -r requirements-freeze.txt
 
 COPY context/* .
 
-ENTRYPOINT ["python", "/main.py"]
+CMD ["python", "/main.py"]
diff --git a/containers/extract-summary/pipeline.cwl b/containers/extract-summary/pipeline.cwl
@@ -9,7 +9,9 @@ requirements:
     types:
       - $import: ./options.yml
 
-baseCommand: python /main.py
+baseCommand: python
+arguments:
+  - /main.py
 
 inputs:
   annotations:

diff --git a/containers/popv/Dockerfile b/containers/popv/Dockerfile
@@ -14,4 +14,4 @@ RUN pip install -r requirements-freeze.txt
 
 COPY context/* .
 
-ENTRYPOINT ["python", "/main.py"]
+CMD ["python", "/main.py"]
diff --git a/containers/popv/pipeline.cwl b/containers/popv/pipeline.cwl
@@ -9,7 +9,9 @@ requirements:
     types:
       - $import: ./options.yml
 
-baseCommand: python /main.py
+baseCommand: python
+arguments:
+  - /main.py
 
 inputs:
   matrix:

diff --git a/containers/preprocess/Dockerfile b/containers/preprocess/Dockerfile
@@ -5,4 +5,4 @@ RUN pip install -r requirements-freeze.txt
 
 COPY context/* .
 
-ENTRYPOINT ["python", "/main.py"]
+CMD ["python", "/main.py"]
diff --git a/containers/preprocess/pipeline.cwl b/containers/preprocess/pipeline.cwl
@@ -9,7 +9,9 @@ requirements:
     types:
       - $import: ./options.yml
 
-baseCommand: python /main.py
+baseCommand: python
+arguments:
+  - /main.py
 
 inputs:
   matrix: