feat: Integrate AutoACMG microservice (#66) (#67)

.github/workflows/ci.yml

@@ -57,6 +57,8 @@ jobs:
           mkdir -p .ci/volumes/rabbitmq/data
           mkdir -p .ci/volumes/redis/data
           mkdir -p .ci/volumes/reev-static/data
+          mkdir -p .ci/volumes/seqrepo/local
+          mkdir -p .ci/volumes/seqrepo/master
 
       - name: Prepare configuration
         run: |

docker-compose.override.yml-dev

@@ -50,6 +50,11 @@ services:
     ports:
       - "3006:8080"
 
+  # map auto-acmg to port 3007
+  auto-acmg:
+    ports:
+      - "3007:8080"
+
   # disable traefik
   traefik:
     deploy:

docker-compose.yml

@@ -196,6 +196,26 @@ services:
     image: "${image_base:-ghcr.io/bihealth}/${image_cada_prio_name:-cada-prio}:\
       ${image_cada_prio_version:-main}"
 
+  # -- auto-acmg --------------------------------------------------------------
+  #
+  # auto-acmg provides automatic ACMG classification
+
+  auto-acmg:
+    <<: *service_internal
+    container_name: auto-acmg
+    hostname: auto-acmg
+    image: "${image_base:-ghcr.io/bihealth}/${image_auto_acmg_name:-auto-acmg}:\
+      ${image_auto_acmg_version:-main}"
+    volumes:
+      - type: bind
+        source: ${volumes_basedir:-./.dev/volumes}/seqrepo/local
+        target: /usr/local/share/seqrepo
+      - type: bind
+        source: ${volumes_basedir:-./.dev/volumes}/seqrepo/master
+        target: /home/auto-acmg/seqrepo/master
+    env_file:
+      - .env
+
   # -- PostgreSQL Server -----------------------------------------------------
   #
   # We use the default configuration, but mount a volume for the data for

env.tpl

@@ -16,6 +16,9 @@ FIRST_SUPERUSER_PASSWORD=SECURITY-ALERT-REPLACE-THIS
 # Enable this on production only.
 # CLINVAR_USE_PRODUCTION=1
 
+# AutoACMG
+SEQREPO_DATA_DIR=/home/user/seqrepo/master
+
 # Postgres
 POSTGRES_SERVER=postgres
 POSTGRES_USER=reev