varfish-org · holtgrewe · Feb 1, 2024 · Jan 31, 2024 · Jan 31, 2024 · Feb 1, 2024
diff --git 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_<thetoken>
 
 $ cd utils/terraform

diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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