Merge branch 'main' into dev

Author: bpblanken

.github/workflows/prod-release.yml

@@ -93,3 +93,30 @@ jobs:
       - name: Build and push images
         run: |-
           gcloud builds submit --quiet --substitutions="COMMIT_SHA=${{ github.event.workflow_run.head_sha }},_CUSTOM_BRANCH_TAG=gcloud-prod" --config .cloudbuild/docker.cloudbuild.yaml --gcs-log-dir=gs://seqr-github-actions-logs/logs .
+
+  helm_update:
+    runs-on: ubuntu-latest
+    needs: docker
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          repository: broadinstitute/seqr-helm
+          ref: main
+          persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
+          fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+
+      - name: Update appVersion in seqr Chart file
+        uses: mikefarah/yq@v4.22.1
+        with:
+          cmd: >
+            yq -i '.appVersion = "${{ github.event.workflow_run.head_sha }}"' charts/pipeline-runner/Chart.yaml
+
+      - name: Commit and Push changes
+        uses: Andro999b/push@v1.3
+        with:
+          repository: broadinstitute/seqr-helm
+          branch: main
+          github_token: ${{ secrets.SEQR_VERSION_UPDATE_TOKEN }}
+          author_email: ${{ github.actor }}@users.noreply.github.com
+          author_name: tgg-automation
+          message: "Update pipeline-runner chart appVersion to ${{ github.event.workflow_run.head_sha }}"

v03_pipeline/bin/rsync_reference_data.bash

@@ -17,4 +17,11 @@ case $REFERENCE_GENOME in
 esac
 
 mkdir -p $REFERENCE_DATASETS_DIR/$REFERENCE_GENOME;
+
+if [ -f "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS ]; then
+   echo "Skipping rsync because already successful"
+   exit 0;
+fi
+
 gsutil -m rsync -rd "gs://seqr-reference-data/v03/$REFERENCE_GENOME" $REFERENCE_DATASETS_DIR/$REFERENCE_GENOME
+touch "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS

v03_pipeline/lib/model/environment.py

@@ -35,7 +35,7 @@
     'HAIL_BACKEND_SERVICE_HOSTNAME',
     'hail-search',
 )
-HAIL_BACKEND_SERVICE_PORT = int(os.environ.get('HAIL_BACKEND_SERVICE_PORT', '6000'))
+HAIL_BACKEND_SERVICE_PORT = int(os.environ.get('HAIL_BACKEND_SERVICE_PORT', '5000'))
 CLINGEN_ALLELE_REGISTRY_LOGIN = os.environ.get('CLINGEN_ALLELE_REGISTRY_LOGIN', '')
 CLINGEN_ALLELE_REGISTRY_PASSWORD = os.environ.get(
     'CLINGEN_ALLELE_REGISTRY_PASSWORD',