bioinformatics_platform/.env.example at dev · phiHelix-BioTech/bioinformatics_platform · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
# ── Database ──────────────────────────────────────────────────────────────────
DATABASE_URL=postgresql://bioplatform:bioplatform@postgres:5432/bioplatform
POSTGRES_USER=bioplatform
POSTGRES_PASSWORD=bioplatform
POSTGRES_DB=bioplatform

# ── Redis / Celery ─────────────────────────────────────────────────────────────
CELERY_BROKER_URL=redis://redis:6379/0
CELERY_RESULT_BACKEND=redis://redis:6379/0

# ── Storage ────────────────────────────────────────────────────────────────────
STORAGE_BACKEND=local          # local | s3
# S3-compatible endpoint override (leave empty for native AWS S3)
# Huawei OBS: https://obs.tr-west-1.myhuaweicloud.com
# Turkcell nDepo: your nDepo endpoint
S3_ENDPOINT_URL=

# ── Nextflow ───────────────────────────────────────────────────────────────────
NEXTFLOW_BACKEND=mock          # mock | local | awsbatch | turkishcloud
NEXTFLOW_PROFILE=docker        # docker | singularity  (local mode only)

# ── Other runners ──────────────────────────────────────────────────────────────
SNAKEMAKE_BACKEND=mock         # mock | local | awsbatch | turkishcloud
BIOSCRIPT_BACKEND=mock         # mock | local | awsbatch | turkishcloud
CUSTOM_BACKEND=mock            # mock | awsbatch

# ── Mutation Assessment ────────────────────────────────────────────────────────
ASSESSMENT_GENOME=hg38         # hg19 | hg38
OMIM_API_KEY=                  # free academic key at omim.org/api
ORPHANET_API_KEY=              # free key at orphacode.org

# ── Auth / Security ────────────────────────────────────────────────────────────
JWT_SECRET=change-me-in-production-with-a-random-secret
JWT_ACCESS_EXPIRY_MINUTES=15
JWT_REFRESH_EXPIRY_DAYS=7
MAX_LOGIN_ATTEMPTS=5
LOCKOUT_MINUTES=30
MFA_ISSUER=BioplatformMD

# ── Upload limits ──────────────────────────────────────────────────────────────
MAX_UPLOAD_SIZE_BYTES=10737418240   # 10 GB

# ── Data retention (KVKK / GDPR) ──────────────────────────────────────────────
RETENTION_ENABLED=false
RAW_FILE_RETENTION_DAYS=30
REPORT_RETENTION_DAYS=1825     # 5 years

# ── AWS (required when NEXTFLOW_BACKEND=awsbatch or STORAGE_BACKEND=s3) ───────
AWS_ACCESS_KEY_ID=
AWS_SECRET_ACCESS_KEY=
AWS_REGION=us-east-1
S3_BUCKET=
BATCH_JOB_QUEUE=bioplatform-default
BATCH_JOB_ROLE_ARN=

# ── Turkish Cloud — Huawei ECS (tr-west-1, Istanbul) ──────────────────────────
COMPUTE_PROVIDERS=huawei,turkcell,cloudsigma
HUAWEI_AK=
HUAWEI_SK=
HUAWEI_PROJECT_ID=
HUAWEI_REGION=tr-west-1
HUAWEI_VPC_ID=
HUAWEI_SUBNET_ID=
HUAWEI_SECURITY_GROUP_ID=
HUAWEI_IMAGE_ID=               # Ubuntu 22.04 base image ID in tr-west-1
HUAWEI_FLAVOR_DEFAULT=c7n.2xlarge.4
HUAWEI_OBS_ENDPOINT=https://obs.tr-west-1.myhuaweicloud.com

# ── Turkish Cloud — Turkcell Bulut (VMware vCD) ────────────────────────────────
TURKCELL_VCD_URL=https://svm.turkcellbulut.com
TURKCELL_VCD_ORG=
TURKCELL_VCD_VDC=
TURKCELL_VCD_USER=
TURKCELL_VCD_PASSWORD=
TURKCELL_VCD_NETWORK=
TURKCELL_VCD_CATALOG=
TURKCELL_VCD_TEMPLATE=
TURKCELL_NDEP0_ENDPOINT=
TURKCELL_NDEP0_ACCESS_KEY=
TURKCELL_NDEP0_SECRET_KEY=

# ── Turkish Cloud — CloudSigma / Siaflex (Izmir) ──────────────────────────────
CLOUDSIGMA_API_ENDPOINT=https://siaflex.cloud/api/2.0
CLOUDSIGMA_USERNAME=
CLOUDSIGMA_PASSWORD=

# ── Payments — Stripe ──────────────────────────────────────────────────────────
STRIPE_SECRET_KEY=             # sk_test_... or sk_live_...
STRIPE_WEBHOOK_SECRET=         # whsec_...
APP_BASE_URL=http://localhost:5173

# ── Payments — iyzico (Turkish gateway) ───────────────────────────────────────
IYZICO_API_KEY=
IYZICO_SECRET_KEY=
IYZICO_BASE_URL=https://sandbox.iyzipay.com
IYZICO_USD_TO_TRY_RATE=33.0

# ── Email ──────────────────────────────────────────────────────────────────────
EMAIL_PROVIDER=log             # log | ses | smtp
EMAIL_FROM=noreply@bioplatform.io
SMTP_HOST=
SMTP_PORT=587
SMTP_USER=
SMTP_PASSWORD=

# ── Observability ──────────────────────────────────────────────────────────────
SENTRY_DSN=

# ── Runtime ────────────────────────────────────────────────────────────────────
DEBUG=true
PUBLIC_BASE_URL=http://localhost:8000
ALLOWED_ORIGINS=http://localhost:5173,http://localhost:3000