environment.yml

channels:
  - conda-forge
  - bioconda
  - defaults

name: snappy_env

dependencies:

  # Fundamentals
  - python
  - pip
  - git-lfs

  # Snakemake is used for providing the actual wrapper calling functionality
  - snakemake >=7.0.2

  # Additional libraries used by snappy
  - ruamel.yaml             # Nice, round-trip enabled YAML parsing
  - fasteners               # File-based locks
  - termcolor               # Helpful for CLIs
  - matplotlib              # Required for plotting
  - jinja2                  # Jinja 2 template rendering

  # Bioinformatics-related libraries used by snappy
  - htslib==1.15            # From previous environment.yml
  - bcftools==1.15          # From previous environment.yml
  - samtools==1.15
  - vcfpy                   # Library for working with VCF files
  - pysam                   # Support for vcfpy
  - pytabix                 # Support for vcfpy

  # Parsing of ISA-tab
  - altamisa

  # CUBI libraries required by snappy (installed through pip)
  - pip:
    - varfish-cli
    - biomedsheets