diff --git a/README.md b/README.md index 75de264..7c0e1da 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # VarFish Docker Compose Configuration -This repository contains the [Docker Compose](https://docs.docker.com/compose/) configuration for the [VarFish Server](https://github.com/bihealth/varfish-server). +This repository contains the [Docker Compose](https://docs.docker.com/compose/) configuration for the [VarFish Server](https://github.com/varfish-org/varfish-server). ## Development Setup @@ -29,7 +29,7 @@ Instructions can be found [here on the Docker.com website](https://docs.docker.c First, clone the repository: ```bash session -git clone git@github.com:bihealth/varfish-docker-compose-ng.git +git clone git@github.com:varfish-org/varfish-docker-compose-ng.git ``` From here on, the commands should be executed from within this repository (`cd varfish-docker-compose-ng`). @@ -229,7 +229,7 @@ To User: the-user ### Managing GitHub Project with Terraform ```bash session -$ export GITHUB_OWNER=bihealth +$ export GITHUB_OWNER=varfish-org $ export GITHUB_TOKEN=ghp_ $ cd utils/terraform diff --git a/docker-compose.override.yml-cadd b/docker-compose.override.yml-cadd index 998cc25..46530a9 100644 --- a/docker-compose.override.yml-cadd +++ b/docker-compose.override.yml-cadd @@ -23,7 +23,7 @@ services: cadd-rest-api-server: <<: *service_default - image: "${image_cadd_name-bihealth/cadd-rest-api}:${image_cadd_version-0.3.4-0}" + image: "${image_cadd_name-varfish-org/cadd-rest-api}:${image_cadd_version-0.3.4-0}" env_file: cadd-rest-api.env command: - wsgi @@ -37,7 +37,7 @@ services: <<: *service_default deploy: replicas: 5 - image: "${image_cadd_name-bihealth/cadd-rest-api}:${image_cadd_version-0.3.4-0}" + image: "${image_cadd_name-varfish-org/cadd-rest-api}:${image_cadd_version-0.3.4-0}" env_file: cadd-rest-api.env command: - celeryd diff --git a/docker-compose.override.yml-dev b/docker-compose.override.yml-dev index a85f22a..394f9aa 100644 --- a/docker-compose.override.yml-dev +++ b/docker-compose.override.yml-dev @@ -55,3 +55,26 @@ services: redis: deploy: replicas: 0 + + # disable varfish containers + varfish-web: + deploy: + replicas: 0 + varfish-celerybeat: + deploy: + replicas: 0 + varfish-celeryd-default: + deploy: + replicas: 0 + varfish-celeryd-query: + deploy: + replicas: 0 + varfish-celeryd-import: + deploy: + replicas: 0 + varfish-celeryd-export: + deploy: + replicas: 0 + varfish-celeryd-maintenance: + deploy: + replicas: 0 diff --git a/docker-compose.yml b/docker-compose.yml index 64a6f7a..db44a4d 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -25,7 +25,7 @@ x-service-varfish-static-data-default: &service_static_data_default # Default service definition for services with the `varfish-server` image. x-service-varfish-server-default: &service_varfish_server_default <<: *service_default - image: "${image_base-ghcr.io/bihealth}/\ + image: "${image_base-ghcr.io/varfish-org}/\ ${image_varfish_name:-varfish-server}:${image_varfish_version:-main}" env_file: .env @@ -180,7 +180,7 @@ services: <<: *service_static_data_default container_name: mehari hostname: mehari - image: "${image_base:-ghcr.io/bihealth}/${image_mehari_name:-mehari}:\ + image: "${image_base:-ghcr.io/varfish-org}/${image_mehari_name:-mehari}:\ ${image_mehari_version:-latest}" # -- Viguno ---------------------------------------------------------------- @@ -192,7 +192,7 @@ services: <<: *service_static_data_default container_name: viguno hostname: viguno - image: "${image_base:-ghcr.io/bihealth}/${image_viguno_name:-viguno}:\ + image: "${image_base:-ghcr.io/varfish-org}/${image_viguno_name:-viguno}:\ ${image_viguno_version:-latest}" # -- Annonars --------------------------------------------------------------- @@ -203,8 +203,8 @@ services: <<: *service_static_data_default container_name: annonars hostname: annonars - image: "${image_base:-ghcr.io/bihealth}/${image_annonars_name:-annonars}:\ - ${image_annonars_version:-latest}" + image: "${image_base:-ghcr.io/varfish-org}/\ + ${image_annonars_name:-annonars}:${image_annonars_version:-latest}" # -- PostgreSQL Server ----------------------------------------------------- # diff --git a/download-data.sh b/download-data.sh index bf6ff78..7d3b5e8 100644 --- a/download-data.sh +++ b/download-data.sh @@ -23,7 +23,7 @@ export DIR_PREFIX=${DIR_PREFIX-.dev} # Overall static data directory. export DATA_DIR=${DATA_DIR-$DIR_PREFIX/volumes/$STATIC_INFIX/data} # S3 endpoing URL. -export S3_ENDPOINT_URL=https://ceph-s3-public.cubi.bihealth.org +export S3_ENDPOINT_URL=https://ceph-s3-public.cubi.varfish-org.org # -- Versions ----------------------------------------------------------------- @@ -514,7 +514,7 @@ mkdir -p $DATA_DIR/download/mehari-data-txs-grch3{7,8} for ext in .zst .zst.sha256 .zst.report .zst.report.sha256; do for release in grch37 grch38; do wget -q -c -O $DATA_DIR/download/mehari-data-txs-$release/mehari-data-txs-$release-$V_MEHARI_TXS.bin$ext \ - https://github.com/bihealth/mehari-data-tx/releases/download/v$V_MEHARI_TXS/mehari-data-txs-$release-$V_MEHARI_TXS.bin$ext + https://github.com/varfish-org/mehari-data-tx/releases/download/v$V_MEHARI_TXS/mehari-data-txs-$release-$V_MEHARI_TXS.bin$ext done done @@ -527,9 +527,9 @@ done log_info "- clinvar" wget -q -c -O /tmp/annonars-clinvar-minimal-grch37-$V_ANNONARS_DATA_CLINVAR_CLINVAR+$V_ANNONARS_DATA_CLINVAR_ANNONARS.tar.gz \ - https://github.com/bihealth/annonars-data-clinvar/releases/download/annonars-data-clinvar-$V_ANNONARS_DATA_CLINVAR_CLINVAR/annonars-clinvar-minimal-grch37-$V_ANNONARS_DATA_CLINVAR_CLINVAR+$V_ANNONARS_DATA_CLINVAR_ANNONARS.tar.gz + https://github.com/varfish-org/annonars-data-clinvar/releases/download/annonars-data-clinvar-$V_ANNONARS_DATA_CLINVAR_CLINVAR/annonars-clinvar-minimal-grch37-$V_ANNONARS_DATA_CLINVAR_CLINVAR+$V_ANNONARS_DATA_CLINVAR_ANNONARS.tar.gz wget -q -c -O /tmp/annonars-clinvar-minimal-grch38-$V_ANNONARS_DATA_CLINVAR_CLINVAR+$V_ANNONARS_DATA_CLINVAR_ANNONARS.tar.gz \ - https://github.com/bihealth/annonars-data-clinvar/releases/download/annonars-data-clinvar-$V_ANNONARS_DATA_CLINVAR_CLINVAR/annonars-clinvar-minimal-grch38-$V_ANNONARS_DATA_CLINVAR_CLINVAR+$V_ANNONARS_DATA_CLINVAR_ANNONARS.tar.gz + https://github.com/varfish-org/annonars-data-clinvar/releases/download/annonars-data-clinvar-$V_ANNONARS_DATA_CLINVAR_CLINVAR/annonars-clinvar-minimal-grch38-$V_ANNONARS_DATA_CLINVAR_CLINVAR+$V_ANNONARS_DATA_CLINVAR_ANNONARS.tar.gz tar -C $DATA_DIR/download/annonars/ \ -xf /tmp/annonars-clinvar-minimal-grch37-$V_ANNONARS_DATA_CLINVAR_CLINVAR+$V_ANNONARS_DATA_CLINVAR_ANNONARS.tar.gz @@ -544,7 +544,7 @@ ln -sr $DATA_DIR/download/annonars/annonars-clinvar-minimal-grch38-$V_ANNONARS_D $DATA_DIR/annonars/grch38/clinvar wget -q -c -O /tmp/annonars-clinvar-genes-$V_ANNONARS_DATA_CLINVAR_CLINVAR+$V_ANNONARS_DATA_CLINVAR_ANNONARS.tar.gz \ - https://github.com/bihealth/annonars-data-clinvar/releases/download/annonars-data-clinvar-$V_ANNONARS_DATA_CLINVAR_CLINVAR/annonars-clinvar-genes-$V_ANNONARS_DATA_CLINVAR_CLINVAR+$V_ANNONARS_DATA_CLINVAR_ANNONARS.tar.gz + https://github.com/varfish-org/annonars-data-clinvar/releases/download/annonars-data-clinvar-$V_ANNONARS_DATA_CLINVAR_CLINVAR/annonars-clinvar-genes-$V_ANNONARS_DATA_CLINVAR_CLINVAR+$V_ANNONARS_DATA_CLINVAR_ANNONARS.tar.gz tar -C $DATA_DIR/download/annonars \ -xf /tmp/annonars-clinvar-genes-$V_ANNONARS_DATA_CLINVAR_CLINVAR+$V_ANNONARS_DATA_CLINVAR_ANNONARS.tar.gz @@ -553,9 +553,9 @@ ln -sr $DATA_DIR/download/annonars/annonars-clinvar-genes-$V_ANNONARS_DATA_CLINV $DATA_DIR/annonars/clinvar-genes wget -q -c -O /tmp/annonars-clinvar-sv-grch37-$V_ANNONARS_DATA_CLINVAR_CLINVAR+$V_ANNONARS_DATA_CLINVAR_ANNONARS.tar.gz \ - https://github.com/bihealth/annonars-data-clinvar/releases/download/annonars-data-clinvar-$V_ANNONARS_DATA_CLINVAR_CLINVAR/annonars-clinvar-sv-grch37-$V_ANNONARS_DATA_CLINVAR_CLINVAR+$V_ANNONARS_DATA_CLINVAR_ANNONARS.tar.gz + https://github.com/varfish-org/annonars-data-clinvar/releases/download/annonars-data-clinvar-$V_ANNONARS_DATA_CLINVAR_CLINVAR/annonars-clinvar-sv-grch37-$V_ANNONARS_DATA_CLINVAR_CLINVAR+$V_ANNONARS_DATA_CLINVAR_ANNONARS.tar.gz wget -q -c -O /tmp/annonars-clinvar-sv-grch38-$V_ANNONARS_DATA_CLINVAR_CLINVAR+$V_ANNONARS_DATA_CLINVAR_ANNONARS.tar.gz \ - https://github.com/bihealth/annonars-data-clinvar/releases/download/annonars-data-clinvar-$V_ANNONARS_DATA_CLINVAR_CLINVAR/annonars-clinvar-sv-grch38-$V_ANNONARS_DATA_CLINVAR_CLINVAR+$V_ANNONARS_DATA_CLINVAR_ANNONARS.tar.gz + https://github.com/varfish-org/annonars-data-clinvar/releases/download/annonars-data-clinvar-$V_ANNONARS_DATA_CLINVAR_CLINVAR/annonars-clinvar-sv-grch38-$V_ANNONARS_DATA_CLINVAR_CLINVAR+$V_ANNONARS_DATA_CLINVAR_ANNONARS.tar.gz tar -C $DATA_DIR/download/annonars/ \ -xf /tmp/annonars-clinvar-sv-grch37-$V_ANNONARS_DATA_CLINVAR_CLINVAR+$V_ANNONARS_DATA_CLINVAR_ANNONARS.tar.gz tar -C $DATA_DIR/download/annonars/ \ @@ -576,8 +576,8 @@ wget -q -c \ https://github.com/SACGF/cdot/releases/download/v$V_DOTTY_CDOT_VERSION/cdot-$V_DOTTY_CDOT_VERSION.refseq.grch37.json.gz \ https://github.com/SACGF/cdot/releases/download/v$V_DOTTY_CDOT_VERSION/cdot-$V_DOTTY_CDOT_VERSION.refseq.grch38.json.gz wget -q -c \ - https://github.com/bihealth/dotty/releases/download/v$V_DOTTY_SEQREPO/seqrepo.tar.gz-00 \ - https://github.com/bihealth/dotty/releases/download/v$V_DOTTY_SEQREPO/seqrepo.tar.gz-01 + https://github.com/varfish-org/dotty/releases/download/v$V_DOTTY_SEQREPO/seqrepo.tar.gz-00 \ + https://github.com/varfish-org/dotty/releases/download/v$V_DOTTY_SEQREPO/seqrepo.tar.gz-01 cat seqrepo.tar.gz-?? | tar -xzf - popd >/dev/null @@ -591,7 +591,7 @@ log_info "- cada-prio" mkdir -p $DATA_DIR/download/cada pushd $DATA_DIR/download/cada >/dev/null wget -q -c \ - https://github.com/bihealth/cada-prio-data/releases/download/cada-prio-data-$V_CADA_PRIO_MODEL/cada-prio-model-$V_CADA_PRIO_MODEL+$V_CADA_PRIO_VERSION.tar.gz + https://github.com/varfish-org/cada-prio-data/releases/download/cada-prio-data-$V_CADA_PRIO_MODEL/cada-prio-model-$V_CADA_PRIO_MODEL+$V_CADA_PRIO_VERSION.tar.gz tar -xzf cada-prio-model-$V_CADA_PRIO_MODEL+$V_CADA_PRIO_VERSION.tar.gz popd >/dev/null diff --git a/env.tpl b/env.tpl index 3272159..88704b3 100644 --- a/env.tpl +++ b/env.tpl @@ -61,7 +61,7 @@ GUNICORN_WORKERS=16 # -- Docker Images ----------------------------------------------------------- # Name of the registry server and org to use for our images. -# image_base=ghcr.io/bihealth +# image_base=ghcr.io/varfish-org # Version of the varfish image to use. # image_varfish_version=main