PhyloSOLID/environment.yml at main · douymLab/PhyloSOLID · GitHub

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name: phylosolid_env
channels:
  - conda-forge
  - bioconda
  - r
  - defaults
dependencies:
  # Python base
  - python=3.10
  - pip

  # Core scientific computing - Pin numpy to avoid 2.x incompatibility
  - numpy=1.24.3
  - pandas>=1.3.0
  - scipy>=1.7.0
  - matplotlib>=3.4.0
  - seaborn>=0.11.0

  # Machine learning
  - scikit-learn>=1.0.0
  - joblib>=1.0.0

  # Graph analysis and networks
  - networkx>=2.6.0
  - python-igraph>=0.9.0
  - leidenalg>=0.8.0
  - python-louvain>=0.15
  - anytree>=2.8.0
  - pygraphviz

  # Single-cell analysis
  - scanpy>=1.9.0
  - anndata>=0.8.0

  # Bioinformatics
  - pysam>=0.19.0
  - pybedtools>=0.9.0
  - pyfaidx>=0.7.0
  - biopython>=1.79

  # Spatial analysis
  - geopandas>=0.14.0
  - pysal=1.14.3
  - colorcet>=3.0.0

  # Performance profiling
  - memory-profiler>=0.60.0

  # Parallel processing and utilities
  - tqdm>=4.62.0
  - multiprocess

  # Statistics
  - statsmodels>=0.13.0

  # Phylogenetics related
  - ete3
  - dendropy

  # File handling
  - h5py>=3.4.0
  - hdf5>=1.12.0
  - pytables>=3.6.0

  # Git
  - git

  # R language support
  - r-base=4.3
  - r-essentials
  - r-devtools
  - r-remotes
  - r-ape
  - r-phangorn
  - r-phytools
  - r-phylogram
  - r-reticulate
  - r-dendextend
  - r-pheatmap
  - r-circlize
  - r-ggnewscale
  - r-ggtext
  - r-pals
  - r-Polychrome
  - r-gridextra
  - r-patchwork
  - r-cowplot
  - r-rlang
  - r-pracma
  - r-gtable
  - r-tibble
  - r-sampling
  - r-TreeDist

  # Bioconductor packages
  - bioconductor-treeio
  - bioconductor-annotationdbi
  - bioconductor-org.hs.eg.db
  - bioconductor-complexheatmap
  - bioconductor-ggtree
  - bioconductor-ggtreeextra

  # Pip installed packages
  - pip:
    # Deep learning
    - torch>=1.9.0,<2.0.0

    # Phylogenetics tools
    - scphylo-tools>=0.0.4
    - apted>=1.0.3

    # VCF handling
    - vcfpy>=0.13.0

    # Logging and debugging
    - loguru>=0.5.0

    # Python-R interface
    - rpy2>=3.5.0

    # Interactive visualization
    - plotly>=5.3.0

    # Additional Python packages
    - gitpython>=3.1.0
    - requests>=2.26.0
    - json5>=0.9.0
    - pyyaml>=5.4.0
    - cloudpickle>=2.0.0
    - pytest>=6.2.0
    - black>=21.0.0
    - cogent3
    - hdf5plugin>=3.0.0
    - pickle5>=0.0.11