gnext_platform/.env.example at main · DyHealthNet/gnext_platform · GitHub

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# ============================================
# GNExT Platform Environment Configuration
# ============================================
# Copy this file to .env and customize for your deployment
# cp .env.example .env

# ============================================
# Study Identifier for Deployment
# ============================================
# Used for container names and network (no spaces, lowercase recommended)
STUDY_ACRONYM=your_study

# ============================================
# Study Name and Genome Build
# ============================================
# Display name for your study in the home page as title
VITE_STUDY_NAME="Your Study Name"

# Genome build version (GRCh37 or GRCh38)
VITE_GENOME_BUILD=GRCh37

# Human genome build number (19 for GRCh37, 38 for GRCh38)
VITE_HG_BUILD_NUMBER=19

# ============================================
# Study-Specific Data Paths (Absolute Paths Required)
# ============================================
# Path to phenotype CSV file
PHENO_FILE=/path/to/your/pheno_file.csv

# Directory containing Nextflow pipeline output
NF_DATA_DIR=/path/to/your/nextflow_output/

# ============================================
# Study-Specific Citation Information
# ============================================
# BibTeX citation
VITE_STUDY_BIBTEX_CITATION="@article{your_study_2025,
	title = {Your Study Title},
	journal = {Your Journal},
	author = {Your Author List},
	year = {2025},
	doi = {10.xxxx/your.doi}
}"

# Plain text citation
VITE_STUDY_PLAIN_CITATION="Your Author et al. Your Study Title. Your Journal (2025). https://doi.org/10.xxxx/your.doi"

# DOI link
VITE_STUDY_CITATION_DOI_LINK="https://doi.org/10.xxxx/your.doi"

# ============================================
# Study-Specific Example Data for UI Demonstrations (optional)
# ============================================
# Example trait ID for search demonstrations
VITE_TRAIT_EXAMPLE="your_trait_id"

# Example variant ID for search demonstrations (format: chr_pos_ref/alt)
VITE_VARIANT_EXAMPLE="1_12345678_A/G"

# Example gene ID for search demonstrations
VITE_GENE_EXAMPLE="ENSG00000000001"

# ============================================
# Study-Specific Feature Configuration
# ============================================
# Show MAGMA gene-based analysis (true/false) -> if true, ensure MAGMA data is available from the Nextflow pipeline output
VITE_MAGMA_SHOW=true

# Gene ID format ("symbol" or "ensembl")
VITE_GENE_ID_SPACE="symbol"

# External reference URL for traits (optional)
VITE_TRAIT_EXTERNAL_REF_URL=""

# ============================================
# Study-specific MAGMA Analysis Configuration
# ============================================
# Reference population used for MAGMA analysis -> please add the same as used in Nextflow pipeline
MAGMA_REF_POPULATION="1000 Genomes European"

# Gene location annotation version -> please add the same as used in Nextflow pipeline
MAGMA_REF_GENE_LOCATION="Ensembl v110"

# ============================================
# Typesense Search Configuration
# ============================================
# Generate a secure random key
VITE_TYPESENSE_KEY=your_secure_typesense_api_key_here

# Typesense port (must be unique if running multiple studies)
VITE_TYPESENSE_PORT=8108

# Directory for Typesense data persistence (absolute path required)
TYPESENSE_VOLUME_DIR=/path/to/your/typesense_volume

# Force data re-import on startup (true/false)
FORCE_TYPESENSE_RESET=false

# ============================================
# UI Theming
# ============================================
# Primary theme color (hex code)
VITE_COLOR_PRIMARY="#1976D2"

# Primary dark theme color (hex code)
VITE_COLOR_PRIMARY_DARK="#1565C0"

# ============================================
# Port Configuration
# ============================================
# Backend API port (must be unique if running multiple studies)
VITE_BACKEND_PORT=8000

# Frontend port for production Docker (dev server uses 5173)
VITE_FRONTEND_PORT=80

# ============================================
# Processing Configuration
# ============================================
# Batch size for data import operations
BATCH_SIZE=100000