Ph pd 2514 multiome on terra

.github/workflows/build-cutadapt.yml

@@ -1,6 +1,6 @@
 name: Cutadapt CI
 
-# Controls when the workflow will run
+# Controls when the workflow will run.
 on:
   # Triggers the workflow on push or pull request events but only for the "develop" and "master" branch
   pull_request:
@@ -20,12 +20,13 @@ env:
   # Region-specific Google Docker repository where GOOGLE_PROJECT/REPOSITORY_NAME can be found
   DOCKER_REGISTRY: us.gcr.io
   GCR_PATH: broad-gotc-prod/cutadapt
+  ACR_PATH: cutadapt
   TAG: ${{ github.event.inputs.image_tag || github.head_ref || github.ref_name }}
 
   # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   # The job that builds our container
-  build:
+  build-for-gcr:
     runs-on: ubuntu-latest
     defaults:
       run:
@@ -56,4 +57,29 @@ jobs:
         password: ${{ secrets.GCR_CI_KEY }}
     # Push the image to the Google Docker registry
     - name: Push image
-      run: "docker push ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}"
+      run: "docker push ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}"
+
+  build-for-acr:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: 3rd-party-tools/cutadapt
+    steps:
+    # checkout the repo
+    - name: 'Checkout GitHub Action'
+      uses: actions/checkout@v3
+
+    - name: 'Login via Azure CLI'
+      uses: azure/login@v1
+      with:
+        creds: ${{ secrets.AZURE_CREDENTIALS }}
+
+    - name: 'Build and push image'
+      uses: azure/docker-login@v1
+      with:
+        login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }}
+        username: ${{ secrets.REGISTRY_USERNAME }}
+        password: ${{ secrets.REGISTRY_PASSWORD }}
+    - run: |
+        docker build . -t ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
+        docker push ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}

.github/workflows/build-samtools-dist-bwa.yml

@@ -1,6 +1,6 @@
 name: Samtools Dist BWA Mem 2 Ubuntu CI
 
-# Controls when the workflow will run
+# Controls when the workflow will run.
 on:
   # Triggers the workflow on push or pull request events but only for the "develop" and "master" branch
   pull_request:
@@ -20,12 +20,13 @@ env:
   # Region-specific Google Docker repository where GOOGLE_PROJECT/REPOSITORY_NAME can be found
   DOCKER_REGISTRY: us.gcr.io
   GCR_PATH: broad-gotc-prod/samtools-dist-bwa
+  ACR_PATH: samtools-dist-bwa
   TAG: ${{ github.event.inputs.image_tag || github.head_ref || github.ref_name }}
 
   # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   # The job that builds our container
-  build:
+  build-for-gcr:
     runs-on: ubuntu-latest
     defaults:
       run:
@@ -56,4 +57,29 @@ jobs:
         password: ${{ secrets.GCR_CI_KEY }}
     # Push the image to the Google Docker registry
     - name: Push image
-      run: "docker push ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}"
+      run: "docker push ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}"
+
+  build-for-acr:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: 3rd-party-tools/samtools-dist-bwa
+    steps:
+    # checkout the repo
+    - name: 'Checkout GitHub Action'
+      uses: actions/checkout@v3
+
+    - name: 'Login via Azure CLI'
+      uses: azure/login@v1
+      with:
+        creds: ${{ secrets.AZURE_CREDENTIALS }}
+
+    - name: 'Build and push image'
+      uses: azure/docker-login@v1
+      with:
+        login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }}
+        username: ${{ secrets.REGISTRY_USERNAME }}
+        password: ${{ secrets.REGISTRY_PASSWORD }}
+    - run: |
+        docker build . -t ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
+        docker push ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}

3rd-party-tools/cutadapt/Dockerfile

@@ -1,4 +1,4 @@
-# Adding a platform tag to ensure that images built on ARM-based machines doesn't break pipelines
+# Adding a platform tag to ensure that images built on ARM-based machines doesn't break pipelines.
 FROM --platform=linux/amd64 python:3.7.7
 
 LABEL maintainer="DSP Data Centers <monster@broadinstitute.org>"

3rd-party-tools/samtools-dist-bwa/Dockerfile

@@ -1,4 +1,4 @@
-# Adding a platform tag to ensure that images built on ARM-based machines doesn't break pipelines
+# Adding a platform tag to ensure that images built on ARM-based machines doesn't break pipelines.
 FROM --platform="linux/amd64"  ubuntu:22.04
 
 ENV TERM=xterm-256color