.env.example

# ── Transport ──────────────────────────────────────────────────────────
# MCP_TRANSPORT_TYPE=stdio          # stdio | http (default: stdio)
# MCP_HTTP_PORT=3010                # HTTP port (default: 3010)
# MCP_HTTP_HOST=localhost           # HTTP host (default: localhost)
# MCP_HTTP_ENDPOINT_PATH=/mcp      # HTTP endpoint path (default: /mcp)
# MCP_HTTP_MAX_BODY_BYTES=1048576  # Max request body bytes; 413 over limit, 0 disables (default: 1048576)
# MCP_PUBLIC_URL=                  # Public origin behind a TLS-terminating proxy (e.g. https://mcp.example.com)

# ── Auth ──────────────────────────────────────────────────────────────
# MCP_AUTH_MODE=none                # none | jwt | oauth (default: none)
# MCP_AUTH_SECRET_KEY=              # JWT secret (required for jwt mode)

# ── Storage ───────────────────────────────────────────────────────────
# STORAGE_PROVIDER_TYPE=in-memory   # in-memory | filesystem | supabase | cloudflare-r2 | cloudflare-kv | cloudflare-d1

# ── Session ──────────────────────────────────────────────────────────
# MCP_SESSION_MODE=stateful         # stateful | stateless (default: stateful)

# ── Memory ───────────────────────────────────────────────────────────
# MCP_GC_PRESSURE_INTERVAL_MS=0     # Opt-in forced Bun.gc(true) interval, ms (Bun only). Drains old-gen backlog
                                    # under sustained HTTP load (issue #50). Try 60000 if RSS grows. Default: 0.

# ── Logging ───────────────────────────────────────────────────────────
# MCP_LOG_LEVEL=info                # debug | info | notice | warning | error

# ── Telemetry ─────────────────────────────────────────────────────────
# OTEL_ENABLED=false                          # Enable OpenTelemetry (default: false)
# OTEL_EXPORTER_OTLP_ENDPOINT=               # OTLP endpoint URL (e.g., http://localhost:4318)

# ── DataCanvas (analytical SQL over staged variant/ClinVar lists) ─────
# CANVAS_PROVIDER_TYPE=none         # none | duckdb. Set to duckdb to enable the spill/SQL
                                    # path behind gnomad_list_gene_variants and
                                    # gnomad_search_clinvar. When none, those tools return a
                                    # capped inline preview and gnomad_dataframe_query is
                                    # unavailable. Not available on Cloudflare Workers.

# ── Server-specific (gnomAD) ─────────────────────────────────────────
# GNOMAD_API_BASE_URL=https://gnomad.broadinstitute.org/api  # GraphQL endpoint override
# GNOMAD_DEFAULT_DATASET=gnomad_r4   # Dataset when a call omits it (gnomad_r4|gnomad_r3|gnomad_r2_1|exac)
# GNOMAD_REQUEST_TIMEOUT_MS=30000    # Per-request timeout against the GraphQL endpoint
# GNOMAD_MAX_CONCURRENCY=2           # Cap on concurrent upstream requests — politeness
# GNOMAD_MAX_VARIANT_BATCH=25        # Max variant IDs per gnomad_get_variant call
# GNOMAD_DATAFRAME_DROP_ENABLED=false # Gate the opt-in gnomad_dataframe_drop tool (off by default)

# ── ClinVar (optional second source via NCBI E-utilities) ────────────
# CLINVAR_BASE_URL=https://eutils.ncbi.nlm.nih.gov/entrez/eutils  # NCBI E-utilities base
# NCBI_API_KEY=                      # Optional NCBI key — raises the rate limit from 3 to 10 req/s