script/environment_stats.yml at main · SirLearning/script · GitHub

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name: stats
channels:
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
  - defaults
dependencies:

  # compilers
  - gxx_linux-64
  - gcc_linux-64
  - gfortran_linux-64
  - cmake
  - pkg-config

  # code languages environment
  - python=3.12
  - openjdk=11  # Hail JDK requirement

  # bioinformatics tools
  - seqkit
  - fastqc
  - plink
  - plink2
  - samtools
  - bcftools
  - vcftools
  - bedtools

  # math libraries
  - hdf5
  - h5py

  # complex environment solving python packages
  - numpy
  - pandas
  - scipy
  - scikit-learn
  - matplotlib
  - seaborn
  - statsmodels
  - scanpy
  - fastcluster
  - PyYAML

  # pip packages
  - pip
  - pip:
      - hail   # Conda environment pip fine-grained installation
      - cookiecutter
      - upsetplot
      - -e .   # Editable install of your own python_script package

# 1. can be created with:
# conda env create -f environment_stats.yml
# 2. or update an existing environment with:
# conda env update -f environment_stats.yml