Fix GitHub workflow docker builds (#80)

Fix and separate GitHub actions for docker builds
genomic-medicine-sweden · Sep 15, 2023 · 94d179e · 94d179e
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commit 94d179e
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diff --git a/.github/workflows/build_dockerfile_master.yml b/.github/workflows/build_dockerfile_master.yml
@@ -0,0 +1,65 @@
+name: Build and publish docker images on push to master
+
+on:
+  push:
+    branches:
+      - "master"
+
+jobs:
+  docker-image-push-illumina:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v3
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Get commit hash
+        id: commit
+        uses: prompt/actions-commit-hash@v2
+
+      - name: Build and push Illumina
+        id: docker_build
+        uses: docker/build-push-action@v3
+        with:
+          context: ./
+          file: ./environments/illumina/Dockerfile
+          push: true
+          tags: "genomicmedicinesweden/gms-artic-illumina:${{steps.commit.outputs.short}}, genomicmedicinesweden/gms-artic-illumina:latest"
+
+  docker-image-push-nanopore:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v3
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Get commit hash
+        id: commit
+        uses: prompt/actions-commit-hash@v2
+
+      - name: Build and push Nanopore
+        id: docker_build
+        uses: docker/build-push-action@v3
+        with:
+          context: ./
+          file: ./environments/nanopore/Dockerfile
+          push: true
+          tags: "genomicmedicinesweden/gms-artic-nanopore:${{steps.commit.outputs.short}}, genomicmedicinesweden/gms-artic-nanopore:latest"
diff --git a/.github/workflows/build_dockerfile.yml → ...lows/build_dockerfile_pangolin_master.yml b/.github/workflows/build_dockerfile.yml → ...lows/build_dockerfile_pangolin_master.yml
@@ -1,11 +1,12 @@
-name: Update docker for artic-ncov2019-illumina, artic-ncov2019-nanopore
+name: Build and publish pangolin docker image for master
 
 on:
  schedule:
    - cron: '0 0 * * *'
  push:
     branches:
       - master
+
 jobs:
   get-version:
     runs-on: ubuntu-latest
@@ -60,12 +61,6 @@ jobs:
        id: buildx
        uses: docker/setup-buildx-action@v1
 
-     - name: Check out pipeline code
-       uses: docker/build-push-action@v2
-       with:
-         context: ./
-         file: environments/illumina/Dockerfile
-
      - name: Build new docker image
        shell: bash
        run: |
@@ -74,9 +69,6 @@ jobs:
          pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
          scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
          constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
-         docker build --no-cache -f environments/illumina/Dockerfile -t genomicmedicinesweden/gms-artic-illumina:latest -t genomicmedicinesweden/gms-artic-illumina:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER} .
-         #Build docker for nanopore
-         docker build --no-cache -f environments/nanopore/Dockerfile -t genomicmedicinesweden/gms-artic-nanopore:latest -t genomicmedicinesweden/gms-artic-nanopore:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER} .
          #Build docker for pangolin-check for specific requirements
          docker build --no-cache -f environments/pangolin/Dockerfile -t genomicmedicinesweden/gms-artic-pangolin:latest -t genomicmedicinesweden/gms-artic-pangolin:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER} --build-arg PANGOLIN_VER=v${REPO_VER} .
 
@@ -87,11 +79,6 @@ jobs:
          pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
          scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
          constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
-         docker image push genomicmedicinesweden/gms-artic-illumina:latest
-         docker image push genomicmedicinesweden/gms-artic-illumina:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER}
-         #Push to dockerhub for nanopore
-         docker image push genomicmedicinesweden/gms-artic-nanopore:latest
-         docker image push genomicmedicinesweden/gms-artic-nanopore:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER}
          #Push to dockerhub for pangolin with specific requirements
          docker image push genomicmedicinesweden/gms-artic-pangolin:latest
          docker image push genomicmedicinesweden/gms-artic-pangolin:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER}
diff --git a/.github/workflows/build_dockerfile_pangolin_stage.yml b/.github/workflows/build_dockerfile_pangolin_stage.yml
@@ -0,0 +1,79 @@
+name: Build and publish pangolin docker image on push for tests
+
+on: [push]
+
+jobs:
+  get-version:
+    runs-on: ubuntu-latest
+    steps:
+     - uses: actions/checkout@v2
+     - name: Get current date
+       id: date
+       run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
+     - name: Test with environment variables
+       run: echo $RELEASE_DATE
+       env:
+         RELEASE_DATE: ${{ steps.date.outputs.date }}
+     - name: Fetch pangolin version
+       shell: bash
+       run: |
+         ##Get pangolin-data version
+         curl -sL https://api.github.com/repos/cov-lineages/pangolin-data/releases/latest | \
+         jq -r ".tag_name" > versions/pangolin-data-latest-version.txt
+         pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt)
+         echo $pangolin_data_VER
+
+         ##Get constellations version
+         curl -sL https://api.github.com/repos/cov-lineages/constellations/releases/latest | \
+         jq -r ".tag_name" > versions/constellations-latest-version.txt
+         constellations_VER=$(cat versions/constellations-latest-version.txt)
+         echo $constellations_VER
+
+         ##Get pangolin version
+         curl -sL https://api.github.com/repos/cov-lineages/pangolin/releases/latest | \
+         jq -r ".tag_name" > versions/pangolin-latest-version.txt
+         PANGOLIN_VER=$(cat versions/pangolin-latest-version.txt)
+         echo $PANGOLIN_VER
+
+         ##Get scorpio version
+         curl -sL https://api.github.com/repos/cov-lineages/scorpio/releases/latest | \
+         jq -r ".tag_name" > versions/scorpio-latest-version.txt
+         scorpio_VER=$(cat versions/scorpio-latest-version.txt)
+         echo $scorpio_VER
+
+
+     - name: Check for modified files
+       id: git-check
+       run: echo ::set-output name=modified::$([ -z "`git status --porcelain`" ] && echo "false" || echo "true")
+
+     - name: Login to Docker Hub
+       uses: docker/login-action@v1
+       with:
+         username: ${{ secrets.DOCKER_HUB_USERNAME }}
+         password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+     - name: Set up Docker Buildx
+       id: buildx
+       uses: docker/setup-buildx-action@v1
+
+     - name: Build new docker image
+       shell: bash
+       run: |
+         echo  ${{ steps.date.outputs.date }}
+         REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||')
+         pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
+         scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
+         constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
+         #Build docker for pangolin-check for specific requirements
+         docker build --no-cache -f environments/pangolin/Dockerfile -t genomicmedicinesweden/gms-artic-pangolin-stage:latest -t genomicmedicinesweden/gms-artic-pangolin-stage:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER} --build-arg PANGOLIN_VER=v${REPO_VER} .
+
+     - name: Push Docker image to DockerHub
+       shell: bash
+       run: |
+         REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||')
+         pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
+         scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
+         constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
+         #Push to dockerhub for pangolin with specific requirements
+         docker image push genomicmedicinesweden/gms-artic-pangolin-stage:latest
+         docker image push genomicmedicinesweden/gms-artic-pangolin-stage:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER}
diff --git a/.github/workflows/build_dockerfile_stage.yml b/.github/workflows/build_dockerfile_stage.yml
@@ -0,0 +1,62 @@
+name: Build and publish docker images on push for tests
+
+on: [push]
+
+jobs:
+  docker-image-push-illumina:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v3
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Get commit hash
+        id: commit
+        uses: prompt/actions-commit-hash@v2
+
+      - name: Build and push Illumina
+        id: docker_build
+        uses: docker/build-push-action@v3
+        with:
+          context: ./
+          file: ./environments/illumina/Dockerfile
+          push: true
+          tags: "genomicmedicinesweden/gms-artic-illumina-stage:${{steps.commit.outputs.short}}, genomicmedicinesweden/gms-artic-illumina-stage:latest"
+
+  docker-image-push-nanopore:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v3
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Get commit hash
+        id: commit
+        uses: prompt/actions-commit-hash@v2
+
+      - name: Build and push Nanopore
+        id: docker_build
+        uses: docker/build-push-action@v3
+        with:
+          context: ./
+          file: ./environments/nanopore/Dockerfile
+          push: true
+          tags: "genomicmedicinesweden/gms-artic-nanopore-stage:${{steps.commit.outputs.short}}, genomicmedicinesweden/gms-artic-nanopore-stage:latest"