From dea2c787324960b8da64ddf283ef76e1a43f8323 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Thu, 11 Jan 2024 14:05:59 +0100
Subject: [PATCH] feat: adding templates for exomiser integration (#46)

---
 .github/workflows/ci.yml              |  4 +++
 docker-compose.override.yml-exomiser  | 43 +++++++++++++++++++++++++++
 docker-compose.yml                    |  2 ++
 env.tpl                               |  8 ++++-
 utils/exomiser/application.properties |  3 ++
 5 files changed, 59 insertions(+), 1 deletion(-)
 create mode 100644 docker-compose.override.yml-exomiser
 create mode 100644 utils/exomiser/application.properties

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 365fdcc..f811ae8 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -28,6 +28,10 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v3
 
+      - name: Prepare empty .env file
+        run: |
+          touch .env
+
       - name: Prepare empty volumes
         run: |
           mkdir -p .ci/volumes/postgres/data
diff --git a/docker-compose.override.yml-exomiser b/docker-compose.override.yml-exomiser
new file mode 100644
index 0000000..688b2c1
--- /dev/null
+++ b/docker-compose.override.yml-exomiser
@@ -0,0 +1,43 @@
+# Docker Compose Override YAML fragment that provides a Exomiser REST
+# Prioritiser.
+#
+# Quick Manual:
+#
+# - merge with docker-compose.override.yml
+# - place configuration (from utils/exomiser) in the right plase
+# - place data in the right place
+
+# == Re-useable Definitions ==================================================
+
+# Default service definition for all (incl. postgres/redis/...)
+x-service-default: &service_default
+  networks:
+    - varfish
+  restart: unless-stopped
+
+# == Overide Definitions =====================================================
+
+services:
+  # -- Exomiser --------------------------------------------------------------
+  #
+  # We use the Exomiser REST Prioritizer for phenotype-based prioritization
+
+  exomiser-rest-prioritiser:
+    <<: *service_default
+    image: "${image_exomiser__name-quay.io/biocontainers/exomiser-rest-prioritiser}:\
+      ${image_exomiser__version-13.3.0--hdfd78af_0}"
+    command:
+      - "exomiser-rest-prioritiser"
+      - "-Xmx6G"
+      - "-Xms2G"
+      - "-Dserver.address=0.0.0.0"
+      - "-Dserver.port=80"
+    volumes:
+      - type: bind
+        source: ${config_basedir:-./.dev/config}/exomiser/application.properties
+        target: /application.properties
+        read_only: true
+      - type: bind
+        source: ${volumes_basedir:-./.dev/volumes}/exomiser
+        target: /data
+        read_only: true
diff --git a/docker-compose.yml b/docker-compose.yml
index cef5647..ebbcd6c 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -27,6 +27,8 @@ x-service-varfish-server-default: &service_varfish_server_default
   <<: *service_default
   image: "${image_base-ghcr.io/bihealth}/\
     ${image_varfish_name:-varfish-server}:${image_varfish_version:-main}"
+  env_file:
+    .env
   networks:
     - varfish
   restart: unless-stopped
diff --git a/env.tpl b/env.tpl
index 5ca6957..3272159 100644
--- a/env.tpl
+++ b/env.tpl
@@ -20,7 +20,7 @@ CELERY_BROKER_URL=redis://redis:6379/0
 VARFISH_ENABLE_JANNOVAR=1
 VARFISH_JANNOVAR_REST_API_URL=http://jannovar:80/
 
-VARFISH_ENABLE_EXOMISER_PRIORITISER=1
+VARFISH_ENABLE_EXOMISER_PRIORITISER=0
 VARFISH_ENABLE_EXTRA_ANNOS=1
 VARFISH_EXOMISER_PRIORITISER_API_URL=http://exomiser-rest-prioritiser:80/exomiser/api/prioritise/
 
@@ -129,6 +129,12 @@ GUNICORN_WORKERS=16
 # Version of the nginx image to use.
 # image_nginx_version=1
 
+# Name of the exomiser-rest-prioritiser image to use.
+# image_exomiser__name=quay.io/biocontainers/exomiser-rest-prioritiser
+
+# Version of the exomiser-rest-prioritiser image to use.
+# image_exomiser__version=13.3.0--hdfd78af_0
+
 # -- General Container Configuration -----------------------------------------
 
 # Base directory for configuration.
diff --git a/utils/exomiser/application.properties b/utils/exomiser/application.properties
new file mode 100644
index 0000000..8c832ef
--- /dev/null
+++ b/utils/exomiser/application.properties
@@ -0,0 +1,3 @@
+exomiser.data-directory=/data
+exomiser.phenotype.data-version=2309
+exomiser.phenotype.random-walk-file-name=rw_string_10.mv