dev_env.yml

# This file is used to provide a development environment for Augur.
# <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-file-manually>

# Channel priority should be set per package.
channels:
  - bioconda
  - conda-forge

# While Augur is available as a Conda package, it is not listed here.
# Augur itself and its Python dependencies should be installed via pip.
#
# Version constraints should mirror the Biopython recipe.
# <https://github.com/bioconda/bioconda-recipes/blob/-/recipes/augur/meta.yaml>
dependencies:
  - conda-forge::python >=3.10

  # Augur's non-Python dependencies
  - mafft
  - raxml
  - fasttree
  - iqtree
  - vcftools
  - seqkit
  - conda-forge::sqlite >=3.39,<4

  # Tools used in tests
  - conda-forge::jq
  - conda-forge::tsv-utils