environment.yml

name: BGE-gaplist
channels:
  - conda-forge
  - bioconda
  - defaults

dependencies:
  # Core Python and Snakemake
  - python>=3.10
  - snakemake>=7.25.0
  - graphviz>=8.0.0

  # Core Perl
  - perl>=5.32
  - perl-app-cpanminus
  
  # Essential Perl modules for scripts
  - perl-try-tiny             # Error handling
  - perl-path-tiny           # File operations
  - perl-json-pp             # JSON parsing
  - perl-http-tiny           # HTTP client
  - perl-log-log4perl        # Logging framework
  - perl-datetime            # Date handling
  - perl-moo                 # Modern OO framework
  - perl-namespace-clean     # Clean namespaces
  - perl-type-tiny          # Type checking
  - perl-readonly           # Constant declarations
  - perl-file-path          # Directory operations
  - perl-data-dumper        # Debug output
  - perl-lwp-simple         # Legacy HTTP support
  - perl-time-hires         # High resolution timers
  - perl-unicode-utf8       # UTF-8 handling

  # Testing frameworks and tools
  - perl-test-more          # Testing framework
  - perl-test-exception     # Exception testing
  - perl-test-warn         # Warning testing
  - perl-test-deep         # Deep structure comparison
  - perl-test-differences  # Difference visualization
  - perl-test-pod          # POD testing
  - perl-test-pod-coverage # POD coverage testing
  - perl-file-sharedir     # For Test::File
  - perl-test-file         # File testing

  # Documentation tools
  - perl-pod-usage        # POD processing
  - perl-pod-parser       # POD parsing

  # Development tools
  - perl-local-lib        # Local library management
  - perl-file-slurp       # File reading/writing
  - perl-yaml            # YAML parsing
  - perl-config-tiny     # Configuration handling

variables:
  PERL5LIB: 'lib'
  PERL_UNICODE: 'AS'