diff --git a/.env.ci b/.env.ci index a54eac0..20bf917 100644 --- a/.env.ci +++ b/.env.ci @@ -34,6 +34,12 @@ FLOWER_BASIC_AUTH=admin:flower-password # Name of the registry server and org to use for our images. # image_base=ghcr.io/bihealth +# Name of the dotty image to use. +# image_dotty_name=dotty + +# Version of the dotty image to use. +# image_dotty_version=latest + # Name of the mehari image to use. # image_mehari_name=mehari diff --git a/README.md b/README.md index 9d9427d..9827ac2 100644 --- a/README.md +++ b/README.md @@ -291,6 +291,28 @@ tar -C .dev/volumes/reev-static/data/download/annonars \ ln -sr .dev/volumes/reev-static/data/download/annonars/annonars-clinvar-genes-20230910+0.18.0 \ .dev/volumes/reev-static/data/annonars/clinvar-genes ``` + +To obtain data for dotty + +```bash session +mkdir -p .dev/volumes/reev-static/data/download/dotty +pushd .dev/volumes/reev-static/data/download/dotty +wget \ + https://github.com/SACGF/cdot/releases/download/v0.2.21/cdot-0.2.21.ensembl.grch37.json.gz \ + https://github.com/SACGF/cdot/releases/download/v0.2.21/cdot-0.2.21.ensembl.grch38.json.gz \ + https://github.com/SACGF/cdot/releases/download/v0.2.21/cdot-0.2.21.refseq.grch37.json.gz \ + https://github.com/SACGF/cdot/releases/download/v0.2.21/cdot-0.2.21.refseq.grch38.json.gz +wget \ + https://github.com/bihealth/dotty/releases/download/v0.1.0/seqrepo.tar.gz-00 \ + https://github.com/bihealth/dotty/releases/download/v0.1.0/seqrepo.tar.gz-01 +cat seqrepo.tar.gz-?? | tar xzf - +popd + +mkdir -p .dev/volumes/reev-static/data/dotty +ln -sr .dev/volumes/reev-static/data/download/dotty/{*.json.gz,seqrepo} \ + .dev/volumes/reev-static/data/dotty +``` + ### Setup Configuration The next step step is to create the configuration files in `.dev/config`. @@ -320,6 +342,7 @@ These URLs are used by the REEV application. - Mehari impact prections: http://127.0.0.1:3002/tx/csq?genome-release=grch37&chromosome=17&position=48275363&reference=C&alternative=A - Viguno for TGDS: http://127.0.0.1:3003/hpo/genes?gene_symbol=TGDS - Nginx server with browser tracks http://127.0.0.1:3004/ +- Dotty server with c./n./g. to SPDI resolution http://127.0.0.1:3005/api/v1/to-spdi?q=NM_000059.3:c.274G%3EA Note that the development subset only has variants for a few genes, including BRCA1 (the example above). @@ -344,6 +367,10 @@ We thus summarize some important points here. - In the case of using configuration files, you will have to mount them from the host into the container. - By default, we use "catch-all" configuration based on regular expressions on the host/domain name. +### Dotty + +Dotty (by the REEV authors) provides mapping from c./n./g. notation to SPDI. + ### Mehari Mehari (by the REEV authors) provides information about variants and their effect on individual transcripts. diff --git a/docker-compose.override.yml-dev b/docker-compose.override.yml-dev index 9ac0950..df2d4e9 100644 --- a/docker-compose.override.yml-dev +++ b/docker-compose.override.yml-dev @@ -11,6 +11,7 @@ # - `3002` -- mehari # - `3003` -- viguno # - `3004` -- nginx +# - `3005` -- dotty # - `3020` -- postgres # - `3030` -- redis # - `3031` -- rabbitmq @@ -38,6 +39,11 @@ services: ports: - "3004:80" + # map dotty to port 3005 + nginx: + ports: + - "3005:8080" + # disable traefik traefik: deploy: @@ -67,3 +73,8 @@ services: pgadmin: ports: - "3041:80" + + # no replicas of reev + reev: + deploy: + replicas: 0 diff --git a/docker-compose.yml b/docker-compose.yml index 3ee7629..5d73c0a 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -110,6 +110,20 @@ services: - "traefik.http.services.reev.loadbalancer.server.port=8080" - "traefik.http.routers.reev.tls=true" + # -- Dotty ----------------------------------------------------------------- + # + # Dotty provides translation from c./n./g. notation to SPDI. + + dotty: + <<: *service_reev_default + container_name: dotty + hostname: dotty + image: "${image_base:-ghcr.io/bihealth}/${image_dotty_name:-dotty}:\ + ${image_dotty_version:-latest}" + environment: + DATA_DIR: /data/dotty + + # -- Mehari ---------------------------------------------------------------- # # Mehari provides the transcript-related information. diff --git a/env.tpl b/env.tpl index ffd22e3..5b33366 100644 --- a/env.tpl +++ b/env.tpl @@ -34,6 +34,12 @@ FLOWER_BASIC_AUTH=admin:flower-password # Name of the registry server and org to use for our images. # image_base=ghcr.io/bihealth +# Name of the dotty image to use. +# image_dotty_name=dotty + +# Version of the dotty image to use. +# image_dotty_version=latest + # Name of the mehari image to use. # image_mehari_name=mehari