dib-lab / charcoal

Remove contaminated contigs from genomes using k-mers and taxonomies.
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create a bioconda package and/or install charcoal within the environment.yml #57

Open ctb opened 4 years ago

ctb commented 4 years ago

now that we provide our own (non-snakemake) entry point, charcoal itself needs to be installed in order to run stuff.

in the short term, I think we can use the pip install magic provided by conda to install the latest release of charcoal from PyPI when the base environment is created.

in the medium term, we need a bioconda package! it should be relatively easy to do because this is a pure Python package with minimal dependencies.

taylorreiter commented 2 years ago

I definitely thought charcoal was already pip-installable -- tis not.

I could update the environment.yml to install charcoal from github using pip, which is what i do for all of my snakemake workflows that use charcoal:

channels:
    - conda-forge
    - bioconda
    - defaults
dependencies:
    - python>=3.7,<3.10
    - snakemake-minimal=6.5.1
    - screed
    - click>=7,<8
    - pip
    - mamba
    - sourmash>=4.2.2,<5
    - pip:
      - git+https://github.com/dib-lab/charcoal@latest

I think it would be ideal to make charcoal a bioconda package, but I'm not actual sure what all that entails.