diff --git a/README.md b/README.md index cb22338..ab5bb01 100644 --- 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 index f306895..0488cbf 100644 --- 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 index 0e3841d..44f0fa5 100644 --- 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 index 5b33366..3c9a731 100644 --- 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