name: gubbins_env
channels:
  - conda-forge
  - bioconda
  - defaults
  - r
dependencies:
# python
  - python>=3.8
# installation
  - autoconf
  - automake
  - autoconf-archive
  - pytest
  - pytest-cov
  - lcov
  - check
  - libtool
  - cppunit
  - pkg-config
  - wheel
  - pillow
  - llvm
# algorithm
  - scipy
  - dendropy
  - biopython
  - multiprocess
  - numpy<=1.23.0
  - numba
# phylogenetics
  - raxml=8.2.12
  - iqtree>=2.2
  - rapidnj
  - raxml-ng=1.0.1
  - fasttree=2.1.10
# Scripts
  - ska2>=0.3.0
# R
  - r-argparser
  - r-magrittr
  - r-tidyverse
  - bioconductor-treeio
  - bioconductor-ggtree
  - r-aplot
  - r-patchwork
  - r-cowplot
  - r-rcolorbrewer