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feat: adding cadd-rest-api support via docker-compose.override.yml (#48)
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# Docker Compose Override YAML fragment that provides a CADD REST API | ||
# # Server | ||
# | ||
# Quick Manual: | ||
# | ||
# - merge with docker-compose.override.yml | ||
# - place data in the right place | ||
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# == Re-useable Definitions ================================================== | ||
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# Default service definition for all (incl. postgres/redis/...) | ||
x-service-default: &service_default | ||
networks: | ||
- varfish | ||
restart: unless-stopped | ||
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# == Overide Definitions ===================================================== | ||
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services: | ||
# -- CADD REST API --------------------------------------------------------- | ||
# | ||
# REST API server for CADD sequence variant annotation. | ||
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cadd-rest-api-server: | ||
<<: *service_default | ||
image: "${image_cadd_name-bihealth/cadd-rest-api}:${image_cadd_version-0.3.4-0}" | ||
env_file: cadd-rest-api.env | ||
command: | ||
- wsgi | ||
volumes: | ||
- type: bind | ||
source: ${volumes_basedir:-./.dev/volumes}/cadd-rest-api/db | ||
target: /data/db | ||
read_only: false | ||
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cadd-rest-api-worker: | ||
<<: *service_default | ||
deploy: | ||
replicas: 5 | ||
image: "${image_cadd_name-bihealth/cadd-rest-api}:${image_cadd_version-0.3.4-0}" | ||
env_file: cadd-rest-api.env | ||
command: | ||
- celeryd | ||
volumes: | ||
- type: bind | ||
source: ${volumes_basedir:-./.dev/volumes}/cadd-rest-api/data/annotations | ||
target: /opt/miniconda3/share/cadd-scripts-1.6-0/data/annotations | ||
read_only: true | ||
- type: bind | ||
source: ${volumes_basedir:-./.dev/volumes}/cadd-rest-api/data/prescored | ||
target: /opt/miniconda3/share/cadd-scripts-1.6-0/data/prescored | ||
read_only: true | ||
- type: bind | ||
source: ${volumes_basedir:-./.dev/volumes}/cadd-rest-api/db | ||
target: /data/db | ||
read_only: false |
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# Environment for cadd-rest-api related containers. | ||
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LC_ALL=en_US.UTF-8 | ||
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DATABASE_URL=/data/db/cadd_rest_api.db | ||
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# We can share one redis instance but not the database with another celery. | ||
CELERY_BROKER_URL=redis://redis:6379/1 | ||
# Only one CADD process can be run per CADD container because of using | ||
# Snakemake. | ||
CELERY_WORKERS=1 | ||
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DJANGO_ALLOWED_HOSTS="*" | ||
DJANGO_SECRET_KEY="__DJANGO_SECRET_KEY__" | ||
DJANGO_SETTINGS_MODULE="config.settings.production" | ||
DJANGO_SECURE_SSL_REDIRECT=0 | ||
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CADD_SH=/opt/miniconda3/share/cadd-scripts-1.6-0/CADD.sh | ||
CADD_CONDA=/opt/miniconda3/bin/activate | ||
CADD_TIMEOUT=300 |