singlem.yml

channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  # NOTE: Ensure setup.py is changed in tandem with this file
  - python>=3.7 #, <3.10 # https://github.com/google-research/google-research/issues/779 means scann (at least 1.2.8) fails to install via pip for 3.10. Older python versions than 3.7 may also work, not tested.
  - diamond>=2.1.7 # Getting segmentation fault on test_insert_prefilter otherwise
  - biopython=1.84 # Pinning to be safe, no known issues
  - hmmer=3.2.1 # Pinning to be safe, no known issues
  - orfm=1.3 # Pinning to be safe, no known issues
  - mfqe=0.5.* # Pinning to be safe, no known issues
  - extern=0.4.* # Pinning to be safe, no known issues
  - graftm=0.15.* # 0.15.0+ needed for --translation-table
  - krona=2.8.* # Pinning to be safe, no known issues
  - pplacer=1.1.alpha19 # Pinning to be safe, no known issues
  - sra-tools=3.1.* # Pinning to be safe, no known issues
  - ncbi-ngs-sdk=3.0.* # Pinning to be safe, no known issues
  - sqlite=3.46.* # Pinning to be safe, no known issues
  - squarify=0.4.* # Pinning to be safe, no known issues
  - mafft # mafft has always been good to me, never had changes that broke me
  - seqmagick=0.8.* # Pinning to be safe, no known issues
  - expressbetadiversity=1.0.* # Pinning to be safe, no known issues
  - cd-hit=4.8.* # Pinning to be safe, no known issues
  - fasttree=2.1.* # Pinning to be safe, no known issues
  - fastalite=0.4.* # Pinning to be safe, no known issues
  - jinja2=3.1.* # Pinning to be safe, no known issues
  - pip
  - sqlalchemy=2.0.* # Pinning to be safe, no known issues
  - pandas=2.2.* # Pinning to be safe, no known issues
  - bird_tool_utils_python>=0.4.1,<0.5.0 # 0.4.1+, 0.5.0 to be safe
  - smafa=0.8.* # required for new metapackage smafa db format
  - pyranges=0.1.* # Pinning to be safe, no known issues
  - polars=1.1.* # supplement with taxon genome length requires this, for strip_chars, and group_by
  - prodigal=2.6.* # Pinning to be safe, no known issues
  - tqdm=4.66.* # Pinning to be safe, no known issues
  - pyarrow=16.1.* # Pinning to be safe, no known issues
  - galah >= 0.4.0, <0.5.0 # 0.4.0 is the first version with checkm2 quality inputs, 0.5.0 to be safe
  - pytest # For testing only
  - ipython # For testing only
  - sqlparse # Don't understand why, but this isn't being installed before tests are run on GH actions. Required indirectly (by taxtastic).
  # - python-annoy optional
  # - nmslib # optional
  - zenodo_backpack>=0.3.0, <0.4.0 # required for version specification, <0.4.0 to be safe
  # - pip:
  #   - cmake # Required so scann can be installed and run via pip. Without this, get LD_LIBRARY_PATH error when running pipe.
  #   - scann # optional