environment.yml

# phageFACTor environment
#
# Creates one env with pharokka + phold + foldseek (phold pulls a foldseek binary;
# the same binary serves the custom-FoldSeek step). Phynteny Transformer is best
# installed in its own env (pip) because of setuptools/sklearn pins — see docs.
#
#   micromamba env create -f environment.yml
#   micromamba activate phagefactor
#
# Pin exact versions before publishing (record what your validated run used —
# e.g. foldseek 10.941cd33 as seen in the citro run logs). Left loose here so the
# solver can build on a fresh machine.
name: phagefactor
channels:
  - conda-forge
  - bioconda
dependencies:
  - python>=3.10
  - pharokka
  - phold
  - foldseek
  - mmseqs2
  - pandas
  - biopython
  - openpyxl
  - pyyaml
  - requests          # webAPI search mode (02w)
  - diamond           # mode2 propagation (experimental)
  # --- phynteny: install separately to avoid dependency clashes ---
  # micromamba create -n phynteny python=3.10 && micromamba activate phynteny
  # pip install -U 'setuptools<82' 'scikit-learn>=1.4' phynteny_transformer && install_models