try build with matrix

ktmeaton · Oct 9, 2020 · ab71443 · ab71443
1 parent e7ba66a
commit ab71443
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Showing 3 changed files with 26 additions and 12 deletions.
diff --git a/.github/workflows/docker.yaml b/.github/workflows/docker.yaml
@@ -27,7 +27,6 @@ jobs:
     steps:
       - name: checkout repo
         uses: actions/checkout@v2
-
       #------------------------------------------------------------------------#
       # Check docker and conda changes
       - name: check for changes
@@ -39,20 +38,17 @@ jobs:
           FILES: |
             Dockerfile
             *.yaml
-
-      - name: test
-        run: |
-          echo ${{ matrix.env_name }}
       #------------------------------------------------------------------------#
-      # Plot environment
+      # Build
       - name: build docker image
         if: contains(${{ steps.git-diff.outputs.diff }}, "workflow/envs/${{ matrix.env_name }}/${{ matrix.env_name }}.yaml") || contains(${{ steps.git-diff.outputs.diff }}, "workflow/envs/${{ matrix.env_name }}/Dockerfile")
         run:
           cd workflow/envs/${{ matrix.env_name }};
           docker build --no-cache . -t ktmeaton/plague-phylogeography:${{ matrix.env_name }};
-
-      #- name: push docker image
-      #  if: contains(${{ steps.git-diff.outputs.diff }}, "workflow/envs/plot/plot.yaml") || contains(${{ steps.git-diff.outputs.diff }}, "workflow/envs/plot/Dockerfile")
-      #  run:
-      #    echo "${{ secrets.DOCKERHUB_PASSWORD }}" | docker login -u "${{ secrets.DOCKERHUB_USERNAME }}" --password-stdin;
-      #    docker push ktmeaton/plague-phylogeography:plot
+      #------------------------------------------------------------------------#
+      # Deploy
+      - name: push docker image
+        if: contains(${{ steps.git-diff.outputs.diff }}, "workflow/envs/${{ matrix.env_name }}/${{ matrix.env_name }}.yaml") || contains(${{ steps.git-diff.outputs.diff }}, "workflow/envs/${{ matrix.env_name }}/Dockerfile")
+        run:
+          echo "${{ secrets.DOCKERHUB_PASSWORD }}" | docker login -u "${{ secrets.DOCKERHUB_USERNAME }}" --password-stdin;
+          docker push ktmeaton/plague-phylogeography:${{ matrix.env_name }}
diff --git a/workflow/envs/sra/Dockerfile b/workflow/envs/sra/Dockerfile
@@ -0,0 +1,17 @@
+FROM continuumio/miniconda3
+LABEL authors="Katherine Eaton" \
+      description="Docker image containing dependencies for ktmeaton/plague-phylogeography: sra."
+COPY plot.yaml /
+
+# install mamba and create environment
+RUN conda install -c conda-forge mamba; \
+    mamba env create -f /sra.yaml;
+
+# Cleanup conda to reduce image size
+RUN conda clean -a;
+
+# Activate conda environment on login
+RUN echo "source activate plague-phylogeography-sra" > ~/.bashrc;
+
+ENV BASH_ENV ~/.bashrc
+SHELL ["/bin/bash", "-c"]
diff --git a/workflow/envs/sra.yaml → workflow/envs/sra/sra.yaml b/workflow/envs/sra.yaml → workflow/envs/sra/sra.yaml
@@ -1,3 +1,4 @@
+name: plague-phylogeography-sra
 channels:
   - bioconda
   - conda-forge