CoGA/.env.example at main · CenterForMedicalGeneticsGhent/CoGA · GitHub

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APP_ENV=production
SECRET_KEY=change-me
POSTGRES_HOST=localhost
POSTGRES_PORT=5432
POSTGRES_DB=coga
POSTGRES_USER=coga
POSTGRES_PASSWORD=change-me
# Postgres TLS. POSTGRES_SSLMODE applies to direct DSN connections
# (disable|allow|prefer|require|verify-ca|verify-full). On Cloud SQL, prefer the
# Python Connector for verify-full-grade mTLS over private IP (plain verify-full
# fails the Cloud SQL hostname check). When enabled it supersedes POSTGRES_HOST/SSLMODE.
POSTGRES_SSLMODE=disable
# POSTGRES_USE_CLOUD_SQL_CONNECTOR=false
# POSTGRES_INSTANCE_CONNECTION_NAME=project:region:instance
# CLOUD_SQL_IP_TYPE=PRIVATE
CLICKHOUSE_HOST=localhost
CLICKHOUSE_HTTP_PORT=8123
CLICKHOUSE_DATABASE=coga
CLICKHOUSE_USER=default
CLICKHOUSE_PASSWORD=
# TLS to ClickHouse (TF-13 S-2). Plain HTTP locally; production uses HTTPS:
#   CLICKHOUSE_SECURE=true, CLICKHOUSE_HTTP_PORT=8443, CLICKHOUSE_VERIFY=true.
# For a private CA, set CLICKHOUSE_CA_CERT (inline PEM or a file path) so the server
# cert verifies, and CLICKHOUSE_SERVER_HOST_NAME to a DNS SAN in the cert when
# connecting by IP.
CLICKHOUSE_SECURE=false
CLICKHOUSE_VERIFY=true
# CLICKHOUSE_CA_CERT=
# CLICKHOUSE_SERVER_HOST_NAME=
CORS_ORIGINS=["http://localhost:3000","http://127.0.0.1:3000","http://localhost:5173","http://127.0.0.1:5173","http://localhost:4173","http://127.0.0.1:4173"]
VITE_API_BASE_URL=/api

# Build identity (APP_VERSION / GIT_SHA) is injected at IMAGE-BUILD time via docker
# build-args, NOT here. Do NOT set them in this file: docker-compose `env_file: .env`
# would override the baked-in build identity at runtime and falsify the version frozen
# into signed reports. To stamp a build, export them before `docker compose build`:
#   export APP_VERSION="$(cat VERSION)" GIT_SHA="$(git rev-parse --short=12 HEAD)"

# Optional backend settings
ADMIN_EMAIL=admin@example.com
ADMIN_USERNAME=admin
ADMIN_PASSWORD=change-me
READS_PATH=/data/reads
# Object-storage backend for raw family data (IGV alignments + family-package
# sources): local (default), s3, or gcs.
#   s3:  set S3_BUCKET (+ optional S3_REGION/S3_PREFIX/S3_ENDPOINT_URL).
#   gcs: set GCS_BUCKET (+ optional GCS_PREFIX). Credentials come from Application
#        Default Credentials (Workload Identity on Cloud Run); signed URLs use IAM
#        SignBlob, so the runtime service account needs
#        roles/iam.serviceAccountTokenCreator on itself and the IAM Credentials API.
STORAGE_BACKEND=local
# S3_BUCKET=
# GCS_BUCKET=
# GCS_PREFIX=
# GCS_ENDPOINT_URL= (override for a GCS-compatible endpoint, e.g. fake-gcs-server in tests)
# GCS_PROJECT= (optional; mainly for emulators)
# Roots that Package Import scans for family folders. Local default is
# /data/families; cloud/Terraform deployments point this at a bucket, e.g.
# FAMILY_IMPORT_ROOTS=gs://my-coga-bucket/families  (or s3://...; comma-separate multiple).
FAMILY_IMPORT_ROOTS=/data/families
REFERENCE_FASTA_PATH=
REFERENCE_ALIAS_PATH=
REFERENCE_CYTOBAND_PATH=
GENE_REFERENCE_CLINGEN_VALIDITY_URL=https://search.clinicalgenome.org/kb/gene-validity/download
GENE_REFERENCE_CLINGEN_DOSAGE_URL=https://search.clinicalgenome.org/kb/gene-dosage/download
GENE_REFERENCE_GENCC_URL=https://search.thegencc.org/download/action/submissions-export-csv
GENE_REFERENCE_CLINVAR_GENE_CONDITION_URL=https://ftp.ncbi.nlm.nih.gov/pub/clinvar/gene_condition_source_id
GENE_REFERENCE_DBNSFP_GENE_PATH=/data/ref-data/dbNSFP5.3_gene.gz
GENE_REFERENCE_BOOTSTRAP_ON_STARTUP=true
GITHUB_REPOSITORY=bmenten/coga
GITHUB_REPOSITORY_URL=https://github.com/bmenten/coga
GITHUB_RELEASES_URL=https://github.com/bmenten/coga/releases
GITHUB_ISSUES_URL=https://github.com/bmenten/coga/issues/new/choose
GITHUB_API_TOKEN=
GITHUB_REPO_VISIBILITY=private
GITHUB_RELEASE_CACHE_TTL_SECONDS=300
AZURE_TENANT_ID=
AZURE_CLIENT_ID=
AZURE_ADMIN_OVERRIDE=false

# Optional security / audit tuning
AUDIT_LOG_MODE=async
# none = omit query params, keys = log param names only (recommended; captures
# which filters a search used without their values), sanitized = masked values
AUDIT_LOG_QUERY_STRING_MODE=keys

# Optional frontend overrides for external GitHub links
VITE_GITHUB_REPOSITORY_URL=https://github.com/bmenten/coga
VITE_GITHUB_RELEASES_URL=https://github.com/bmenten/coga/releases
VITE_GITHUB_ISSUES_URL=https://github.com/bmenten/coga/issues/new/choose