Registration form edits/docker dev

docker-compose.dev.yml

@@ -0,0 +1,129 @@
+version: '2.4'
+
+services:
+  postgres:
+    image: postgres:12.6
+    command: postgres -c listen_addresses='*'
+    environment:
+      - PGPORT=5433
+      - POSTGRES_PASSWORD=docker-compose-postgres-password
+    volumes:
+      - ./data/postgres:/var/lib/postgresql/data
+    healthcheck:
+      test: pg_isready -h postgres -U postgres
+      interval: 5s
+      timeout: 10s
+      retries: 100
+
+  redis:
+    image: gcr.io/seqr-project/redis:gcloud-prod
+    healthcheck:
+      test: redis-cli ping
+      interval: 3s
+      timeout: 5s
+      retries: 100
+
+  # elasticsearch:
+  #   image: docker.elastic.co/elasticsearch/elasticsearch:7.16.3
+  #   volumes:
+  #     - /mnt/hpf/data/elasticsearch:/usr/share/elasticsearch/data
+  #   container_name: elasticsearch
+  #   environment:
+  #     - http.host=0.0.0.0
+  #     - discovery.type=single-node
+  #     - cluster.routing.allocation.disk.threshold_enabled=false
+  #   healthcheck:
+  #     test: bash -c "curl -s elasticsearch:9200/_cat/health | grep green"
+  #     interval: 3s
+  #     timeout: 5s
+  #     retries: 100
+  #   ports:
+  #     - 9200:9200
+
+#  kibana:
+#    image: docker.elastic.co/kibana/kibana:7.16.3
+#    environment:
+#      - ELASTICSEARCH_HOSTS=http://elasticsearch:9200
+#    depends_on:
+#      elasticsearch:
+#        condition: service_healthy
+#    healthcheck:
+#      test: bash -c "curl -s kibana:5601 | grep kibana"
+#      interval: 3s
+#      timeout: 5s
+#      retries: 100
+
+  seqr:
+    build: .
+    image: ccm-seqr:dev
+    volumes:
+      - /mnt/hpf/bam_files:/readviz
+      # - ./data/readviz:/readviz
+      - /mnt/hpf/data/seqr_static_files:/seqr_static_files
+      - ./settings.py:/seqr/settings.py
+      - ./gunicorn/gunicorn_config.py:/seqr/gunicorn_config.py
+      - ./logs/django:/var/log/django
+      - ./logs/gunicorn:/var/log/gunicorn
+    ports:
+      - 8000:8000
+    develop:
+      watch:
+        - action: sync
+          path: ./ui
+          target: /seqr/ui
+    environment:
+      - BASE_URL=https://seqr.ccm.sickkids.ca
+      - SEQR_GIT_BRANCH=dev
+      - PYTHONPATH=/seqr
+      - STATIC_MEDIA_DIR=/seqr_static_files
+      - POSTGRES_SERVICE_HOSTNAME=postgres
+      - POSTGRES_SERVICE_PORT=5433
+      - POSTGRES_PASSWORD=docker-compose-postgres-password
+      - ELASTICSEARCH_SERVICE_HOSTNAME=elasticsearch
+      - REDIS_SERVICE_HOSTNAME=redis
+      - KIBANA_SERVICE_HOSTNAME=kibana
+      - PGHOST=postgres
+      - PGPORT=5433
+      - PGUSER=postgres
+      - GUNICORN_WORKER_THREADS=4
+      - ANALYST_USER_GROUP=analyst
+    depends_on:
+      postgres:
+        condition: service_healthy
+      # elasticsearch:
+      #   condition: service_healthy
+      redis:
+        condition: service_healthy
+    healthcheck:
+      test: bash -c "curl -s 'http://localhost:8000' | grep html"
+
+  # pipeline-runner:
+  #   image: gcr.io/seqr-project/pipeline-runner:20220526_130649
+  #   volumes:
+  #     - /mnt/hpf/data/seqr-reference-data:/seqr-reference-data
+  #     - /mnt/hpf/data/vep_data:/vep_data
+  #     - /mnt/hpf/data/input_vcfs:/input_vcfs
+  #     - ./pipeline_runner/download_reference_data.sh:/usr/local/bin/download_reference_data.sh
+  #     - ./pipeline_runner/ensembl-vep-release-104:/ensembl-vep-release-104
+  #     - ./pipeline_runner/entrypoint.sh:/entrypoint.sh
+  #     - ./pipeline_runner/update_clinvar_matrix_table.sh:/usr/local/bin/update_clinvar_matrix_table.sh
+  #     - ./pipeline_runner/update_combined_reference_data.sh:/usr/local/bin/update_combined_reference_data.sh
+  #     - ./pipeline_runner/vep_configs/vep-GRCh37-loftee.json:/vep_configs/vep-GRCh37-loftee.json
+  #     - ./pipeline_runner/vep_configs/vep-GRCh38-loftee.json:/vep_configs/vep-GRCh38-loftee.json
+  #     - ~/.config:/root/.config
+  #   depends_on:
+  #     elasticsearch:
+  #       condition: service_healthy
+
+  # nginx:
+  #   image: nginx
+  #   ports:
+  #     - 80:80
+  #     - 443:443
+  #   depends_on:
+  #     seqr:
+  #       condition: service_healthy
+  #   volumes:
+  #     - ./nginx/conf.d/default.conf:/etc/nginx/conf.d/default.conf
+  #     - ./nginx/certs:/etc/nginx/certs
+  #     - ./logs/nginx:/var/log/nginx