add docker layer caching and nb_conda_kernels

.github/workflows/docker-image.yml

@@ -33,24 +33,29 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Log in to the Container registry
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        uses: docker/login-action@v2
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        uses: docker/metadata-action@v4
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
       - name: prune
         run: docker system prune -af
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        uses: docker/build-push-action@v3
         with:
           context: .
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

Dockerfile

@@ -20,21 +20,7 @@ RUN apt-get update && \
                     man-db \
                     manpages-posix \
                     tree \
-                    -y 
-
-
-# build conda environment with required r packages
-COPY r-bio.yaml /tmp
-RUN mamba env create --file /tmp/r-bio.yaml
-
-# linux hack to remove paths to default R
-RUN rm -rf /opt/conda/bin/R /opt/conda/lib/R && \
-    ln -s /opt/conda/envs/r-bio/bin/R /opt/conda/bin/R
-
-# # create py-bio conda environment with required python packages
-COPY py-bio.yaml /tmp
-RUN mamba env create --file /tmp/py-bio.yaml && \
-    mamba run -n py-bio /bin/bash -c "ipython kernel install --name=py-bio"
+                    -y
 
 # STAR
 RUN wget https://github.com/alexdobin/STAR/archive/2.5.2b.zip -P /tmp && \
@@ -49,23 +35,30 @@ RUN wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5
     chmod 755 /opt/FastQC/fastqc && \
     rm -rf /tmp/fastqc_*
 
-RUN mamba install -c conda-forge bash_kernel
+RUN mamba install -c conda-forge bash_kernel nb_conda_kernels
+
+# build conda environment with required r packages
+COPY r-bio.yaml /tmp
+RUN mamba env create --file /tmp/r-bio.yaml
+
+# linux hack to remove paths to default R
+RUN rm -rf /opt/conda/bin/R /opt/conda/lib/R && \
+    ln -s /opt/conda/envs/r-bio/bin/R /opt/conda/bin/R
+
+# # create py-bio conda environment with required python packages
+COPY py-bio.yaml /tmp
+RUN mamba env create --file /tmp/py-bio.yaml
 
 # create scanpy_2021 conda environment with required python packages
 COPY scanpy_2021.yaml /tmp
-RUN mamba env create --file /tmp/scanpy_2021.yaml && \
-    mamba run -n scanpy_2021 /bin/bash -c "ipython kernel install --name=scanpy_2021"
+RUN mamba env create --file /tmp/scanpy_2021.yaml
 
 COPY spatial-tx.yml /tmp
-RUN mamba env create --file /tmp/spatial-tx.yml && \
-    mamba run -n spatial-tx /bin/bash -c "ipython kernel install --name=spatial-tx"
+RUN mamba env create --file /tmp/spatial-tx.yml
 
 COPY variant_calling.yml /tmp
-RUN mamba env create --file /tmp/variant_calling.yml && \
-    mamba run -n variant_calling /bin/bash -c "ipython kernel install --name=variant_calling"
+RUN mamba env create --file /tmp/variant_calling.yml
 
 RUN yes | unminimize || echo "done"
 
-RUN apt-get install tree -y
-
 USER $NB_USER