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singlem.yml
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/
singlem.yml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- 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
- hmmer
- orfm
- mfqe
- extern
- graftm>=0.15.0 # Version needed for --translation-table
- krona
- pplacer
- sra-tools
- ncbi-ngs-sdk
- sqlite
- squarify
- mafft
- seqmagick
- expressbetadiversity
- cd-hit
- fasttree
- fastalite
- jinja2
- pip
- sqlalchemy
- pandas
- bird_tool_utils_python>=0.4.1
- smafa>=0.8.0 # required for new metapackage smafa db format
- pyranges
- polars>=0.19.3 # supplement with taxon genome length requires this, for strip_chars
- prodigal
- tqdm
- pyarrow
- galah >= 0.4.0 # 0.4.0 is the first version with checkm2 quality inputs
- 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 # required for version specification
# - pip:
# - cmake # Required so scann can be installed and run via pip. Without this, get LD_LIBRARY_PATH error when running pipe.
# - scann # optional