feat: adding cada-prio container

bihealth · Nov 16, 2023 · d510627 · d510627
1 parent d379056
commit d510627
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diff --git a/README.md b/README.md
@@ -317,6 +317,21 @@ ln -sr .dev/volumes/reev-static/data/download/dotty/{*.json.gz,seqrepo} \
   .dev/volumes/reev-static/data/dotty
 ```
 
+To obtain data for cada-prio
+
+```bash session
+mkdir -p .dev/volumes/reev-static/data/download/cada-prio
+pushd .dev/volumes/reev-static/data/download/cada-prio
+wget \
+    https://github.com/bihealth/cada-prio-data/releases/download/cada-prio-data-20231112/cada-prio-model-20231112+0.6.1.tar.gz
+tar -xzf cada-prio-model-20231112+0.6.1.tar.gz 
+popd
+
+mkdir -p .dev/volumes/reev-static/data/cada-prio
+ln -sr .dev/volumes/reev-static/data/download/cada-prio/cada-prio-model-20231112+0.6.1/model/ \
+  .dev/volumes/reev-static/data/cada
+```
+
 ### Setup Configuration
 
 The next step step is to create the configuration files in `.dev/config`.

diff --git a/docker-compose.override.yml-dev b/docker-compose.override.yml-dev
@@ -12,6 +12,7 @@
 #   - `3003` -- viguno
 #   - `3004` -- nginx
 #   - `3005` -- dotty
+#   - `3006` -- cada-prio
 #   - `3020` -- postgres
 #   - `3030` -- redis
 #   - `3031` -- rabbitmq
@@ -44,6 +45,11 @@ services:
     ports:
       - "3005:8080"
 
+  # map cada-prio to port 3006
+  prio:
+    ports:
+      - "3006:8080"
+
   # disable traefik
   traefik:
     deploy:

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -89,6 +89,7 @@ services:
     hostname: reev
     depends_on:
       - annonars
+      - cada-prio
       - dotty
       - mehari
       - nginx
@@ -160,6 +161,17 @@ services:
     image: "${image_base:-ghcr.io/bihealth}/${image_annonars_name:-annonars}:\
       ${image_annonars_version:-latest}"
 
+  # -- cada-prio --------------------------------------------------------------
+  #
+  # cada-prio provides phenotype-based prioritization
+
+  cada-prio:
+    <<: *service_reev_default
+    container_name: cada-prio
+    hostname: cada-prio
+    image: "${image_base:-ghcr.io/bihealth}/${image_cada_prio_name:-cada-prio}:\
+      ${image_cada_prio_version:-main}"
+
   # -- PostgreSQL Server -----------------------------------------------------
   #
   # We use the default configuration, but mount a volume for the data for

diff --git a/env.tpl b/env.tpl
@@ -40,6 +40,12 @@ FLOWER_BASIC_AUTH=admin:flower-password
 # Version of the dotty image to use.
 # image_dotty_version=latest
 
+# Name of the cada-prio image to use.
+# image_cada_prio_name=cada-prio
+
+# Version of the cada-prio image to use.
+# image_cada_prio_version=main
+
 # Name of the mehari image to use.
 # image_mehari_name=mehari