environment-full.yml

name: raptor-full
channels:
  - conda-forge
  - bioconda
  - defaults

dependencies:
  # ==========================================================================
  # Python - v2.2.2 supports Python 3.8-3.12
  # ==========================================================================
  - python>=3.8,<3.13
  
  # ==========================================================================
  # Core Scientific Computing
  # ==========================================================================
  - numpy>=1.19.0
  - pandas>=1.1.0
  - scipy>=1.5.0
  - scikit-learn>=0.24.0
  - joblib>=1.0.0
  
  # ==========================================================================
  # Visualization
  # ==========================================================================
  - matplotlib>=3.3.0
  - seaborn>=0.11.0
  - plotly>=5.0.0
  
  # ==========================================================================
  # Statistics
  # ==========================================================================
  - statsmodels>=0.12.0
  
  # ==========================================================================
  # Configuration Management
  # ==========================================================================
  - pyyaml>=5.3.0
  - toml>=0.10.0
  
  # ==========================================================================
  # CLI and Utilities
  # ==========================================================================
  - click>=7.0
  - colorama>=0.4.0
  - tqdm>=4.50.0
  
  # ==========================================================================
  # Dashboard
  # ==========================================================================
  - streamlit>=1.20.0
  - altair>=4.0.0
  
  # ==========================================================================
  # Development Tools
  # ==========================================================================
  - pytest>=6.0.0
  - pytest-cov>=2.10.0
  - black>=21.0
  - flake8>=3.8.0
  - isort>=5.0.0
  
  # ==========================================================================
  # Documentation
  # ==========================================================================
  - sphinx>=3.5.0
  - sphinx_rtd_theme>=0.5.0
  
  # ==========================================================================
  # MODULE 5: Alignment Tools (Production Pipelines)
  # ==========================================================================
  - star>=2.7.10a              # STAR aligner (gold standard)
  - hisat2>=2.2.1              # HISAT2 (low memory alternative)
  - bowtie2>=2.4.5             # Bowtie2 (for indexing)
  
  # ==========================================================================
  # MODULE 5: Quantification Tools (Production Pipelines)
  # ==========================================================================
  - salmon>=1.9.0              # Salmon pseudo-aligner (RECOMMENDED)
  - kallisto>=0.48.0           # Kallisto pseudo-aligner (fastest)
  - rsem>=1.3.3                # RSEM (isoform quantification)
  - subread>=2.0.3             # featureCounts (gene counting)
  - htseq>=2.0.2               # HTSeq (alternative counter)
  - stringtie>=2.2.1           # StringTie (isoform assembly)
  
  # ==========================================================================
  # Supporting Bioinformatics Tools
  # ==========================================================================
  - samtools>=1.15             # SAM/BAM manipulation
  - bedtools>=2.30.0           # Genomic interval operations
  - sra-tools>=3.0.0           # SRA data download
  
  # ==========================================================================
  # MODULE 6: R and Bioconductor Packages (DE Analysis)
  # ==========================================================================
  - r-base>=4.2.0
  
  # Differential Expression
  - bioconductor-deseq2>=1.38.0
  - bioconductor-edger>=3.40.0
  - bioconductor-limma>=3.54.0
  
  # Import and pre-processing
  - bioconductor-tximport>=1.26.0
  - bioconductor-ballgown>=2.30.0
  
  # Alternative DE methods
  - bioconductor-noiseq>=2.42.0
  - bioconductor-ebseq>=1.38.0
  
  # Sleuth (for Kallisto)
  - bioconductor-sleuth>=0.30.0
  
  # ==========================================================================
  # R Data Handling Packages
  # ==========================================================================
  - r-ggplot2>=3.4.0
  - r-dplyr>=1.1.0
  - r-tidyr>=1.3.0
  - r-readr>=2.1.0
  
  # ==========================================================================
  # Simulation Tools (for testing/benchmarking)
  # ==========================================================================
  - bioconductor-polyester>=1.34.0
  
  # ==========================================================================
  # Additional Data Formats
  # ==========================================================================
  - openpyxl>=3.0.0            # Excel file support
  
  # ==========================================================================
  # MODULE 6b: Data Acquisition (Repository Connectors)
  # ==========================================================================
  - requests>=2.25.0           # HTTP client for GDC, EBI, ENA APIs
  - pyarrow>=8.0.0             # Parquet format for dataset caching
  - biopython>=1.79            # NCBI Entrez search (GEO, SRA)
  
  # ==========================================================================
  # Pip packages and RAPTOR installation
  # ==========================================================================
  - pip
  - pip:
    # Install RAPTOR from PyPI
    - raptor-rnaseq[all]>=2.2.2
    
    # Data Acquisition connectors (pip-only packages)
    - GEOparse>=2.0.0             # GEO dataset parsing
    - mygene>=3.2.0               # Gene ID mapping via MyGene.info
    - combat>=0.3.0               # ComBat batch correction for pooling
    
    # Optional advanced features
    - bayesian-optimization>=1.2.0
    - jinja2>=3.0.0
    - markdown>=3.3.0
    - psutil>=5.8.0
    - colorlog>=6.6.0


# =============================================================================
# USAGE INSTRUCTIONS
# =============================================================================

# Create FULL environment (WARNING: Takes 30-60 minutes!):
#   conda env create -f environment-full.yml

# Activate environment:
#   conda activate raptor-full

# Update environment:
#   conda env update -f environment-full.yml --prune

# Remove environment:
#   conda env remove -n raptor-full

# Verify installation:
#   conda activate raptor-full
#   raptor --version
#   STAR --version
#   salmon --version
#   R --version


# =============================================================================
# NOTES
# =============================================================================

# This is the COMPLETE environment including:
#   ✅ RAPTOR Python package (all features)
#   ✅ All alignment tools (STAR, HISAT2, Salmon, Kallisto)
#   ✅ All quantification tools (RSEM, featureCounts, StringTie)
#   ✅ R with Bioconductor packages (DESeq2, edgeR, limma)
#   ✅ Supporting tools (Samtools, BEDTools, SRA-tools)
#   ✅ Development and documentation tools
#   ✅ Dashboard and visualization
#
# Installation size: ~5-8 GB
# Installation time: 30-60 minutes
#
# For minimal installation (Python only), use: environment.yml
#
# Channels:
#   - conda-forge: Most Python packages, general tools
#   - bioconda: Bioinformatics tools (STAR, Salmon, etc.)
#   - defaults: Anaconda default channel
#
# Platform compatibility:
#   - Linux: Full support ✅
#   - macOS: Full support ✅
#   - Windows: Limited (some bioinformatics tools not available)
#             Use WSL2 or Docker for Windows users


# =============================================================================
# TROUBLESHOOTING
# =============================================================================

# If installation fails:
#   1. Update conda: conda update -n base conda
#   2. Try with specific Python: conda env create -f environment-full.yml python=3.10
#   3. Install in stages (see below)
#
# Stage installation (if full install fails):
#   # Stage 1: Core Python
#   conda env create -f environment.yml
#   
#   # Stage 2: Add bioinformatics tools
#   conda activate raptor
#   conda install -c bioconda star salmon kallisto
#   
#   # Stage 3: Add R packages
#   conda install -c bioconda r-base bioconductor-deseq2 bioconductor-edger
#
# Memory requirements:
#   - Recommend 16+ GB RAM for installation
#   - Some tools (STAR) require 32 GB RAM to run


# =============================================================================
# ALTERNATIVE: Docker
# =============================================================================

# Docker support is planned for a future release (v2.3.0). For now, conda
# (this file) and pip (setup.py / requirements.txt) are the supported
# installation methods.