environment.yml

name: autometa
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - attrs # test-data requirement
  - bedtools
  - biopython
  - black==22.3.0
  - bowtie2
  - diamond>=2.0
  - gdown
  - hdbscan
  - hmmer
  - joblib==1.1.0 # See https://stackoverflow.com/a/73830525/12671809
  - numba>=0.47
  - numpy>=1.13
  - pandas>=1.1
  - parallel
  - pre_commit
  - prodigal # NOTE: 2.5 and 2.6 output format is different for sequence headers
  - pytest
  - pytest-cov
  - pytest-html
  - pytest-repeat
  - pytest-variables
  - python-annoy>=1.11 # required for trimap installation.
  - requests
  - rsync
  - samtools>=1.11
  - scikit-bio
  - scipy==1.8.1 #force scipy 1.8 until scikit-bio updates to 1.9, https://github.com/KwanLab/Autometa/issues/285
  - scikit-learn==0.24 # prevent error from joblib in multiprocessing distance calculations
  - sphinx
  - sphinx_rtd_theme
  - tqdm
  - trimap
  - tsne
  - umap-learn>=0.5 # https://github.com/lmcinnes/umap/releases/tag/0.5.0 : umap, densmap
  - pip
  - pip:
      - pytest-emoji
      - pytest-md