name: bat
channels:
  - conda-forge
  - bioconda
channel_priority: strict
dependencies:
  # R + plotting stack
  - r-base=4.4
  - r-ggplot2=3.5.2
  - bioconductor-ggtree=3.14.0
  - bioconductor-treeio>=1.30.0,<1.31.0
  - r-igraph
  - libxml2
  - glpk
  
  # Direct libraries
  - r-ape
  - r-phytools
  - r-tidytree
  - r-optparse
  - r-broom
  - r-ggnewscale

  # External CLI tools (Bioconda -- not compatible with windows)
  - bioconductor-biostrings
  - trimal
  - clustalo
  - prank
  - fasttree
  - blast
  - mafft >=7,<8
  - hmmer
  - raxml-ng=1.2.2 

  # Python bits used by your pipeline
  - python
  - biopython