Installation

Web Application (Docker)

The fastest way to get started. Requires Docker and Docker Compose.

git clone https://github.com/predomics/predomicsapp-web.git
cd predomicsapp-web
docker compose up -d

Open http://localhost:8001 in your browser. A default admin account is created on first launch.

Environment Variables

Key environment variables (set in docker-compose.yml or .env):

Variable	Default	Description
DATABASE_URL	PostgreSQL connection	Database connection string
SECRET_KEY	auto-generated	JWT signing key
DEFAULT_ADMIN_EMAIL	admin@predomics.local	Initial admin email
DEFAULT_ADMIN_PASSWORD	admin	Initial admin password
PROJECT_DIR	/data/projects	Storage directory for project files

Building from Source

For development or customization:

git clone https://github.com/predomics/predomicsapp-web.git
cd predomicsapp-web

# Backend
cd backend
python -m venv venv
source venv/bin/activate
pip install -r requirements.txt

# Frontend
cd ../frontend
npm install
npm run dev

Python Bindings (gpredomicspy)

Requires the Rust toolchain for compilation.

1. Install Rust

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
source $HOME/.cargo/env

2. Clone and Build

git clone https://github.com/predomics/gpredomics.git
git clone https://github.com/predomics/gpredomicspy.git
cd gpredomicspy
pip install maturin
maturin develop --release

3. Verify Installation

import gpredomicspy
print(gpredomicspy.__version__)

GPU Support (Optional)

For CUDA-based GPU acceleration, ensure you have:

• NVIDIA GPU with CUDA support
• CUDA toolkit installed
• Build with the cuda feature flag:

maturin develop --release --features cuda

R Package

1. Install R

Download and install R from CRAN.

2. Install Dependencies and Package

# Install CRAN dependencies
install.packages(c("doSNOW", "foreach", "snow", "doRNG", "gtools",
                    "glmnet", "pROC", "viridis", "kernlab",
                    "randomForest", "effsize"))

# Install Bioconductor dependency
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("BioQC")

# Install predomicspkg from GitHub
devtools::install_github("predomics/predomicspkg")

3. Verify Installation

library(predomics)
# Should load without errors

System Requirements

Component	Minimum	Recommended
CPU	2 cores	4+ cores
RAM	4 GB	8+ GB
Disk	2 GB	10+ GB (for datasets)
Docker	20.10+	Latest
Python	3.9+	3.11+
R	4.0+	4.3+
Rust	1.70+	Latest stable