environment.yml

name: crisprware
# This installs only the Python environment. The off-target scanner `crispr-ots` is
# a standalone Rust binary distributed via the GitHub Releases page (prebuilt, per
# platform) or built locally with cargo -- download/build it and put it on your PATH.
# See the docs "Installation" page. (`crisprware --ucscgb` can also take an explicit
# --crispr_ots_bin path.)
channels:
  - conda-forge
  - bioconda
  - nodefaults
dependencies:
  - python=3.11
  - biopython>=1.8
  - pybedtools>=0.9
  - matplotlib
  - pybigwig
  - gffread
  - tensorflow=2.15.*   # DeepCpf1 / enseq-DeepCpf1 / DeepSpCas9 / DeepHF
  - h5py>=3.10          # legacy DeepCpf1 .h5 weight loader
  - scikit-learn>=1.3   # enPAM+GB GradientBoostingRegressor
  - joblib>=1.3         # enPAM+GB model serialization
  - bioconda::viennarna>=2.4  # DeepHF RNA folding features (stem, dG)
  - pip
  - pip:
    - lightgbm==3.3.5
    - rs3==0.0.15