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wilkelab / Opfi

A Python package for discovery, annotation, and analysis of gene clusters in genomics or metagenomics data sets.
https://opfi.readthedocs.io/
MIT License
21 stars 5 forks source link

Documentation for optional dependencies #201

Closed afrubin closed 2 years ago

afrubin commented 2 years ago

The documentation at https://opfi.readthedocs.io/en/latest/installation.html#dependencies includes several optional dependencies that might be needed (or required by tests) but does not provide much extra detail.

For example, when would a user want to use GenericRepeatFinder? From what I could tell it is only mentioned on the installation page and is not cited in the paper.

Can the developers provide additional guidance in the documentation as to when someone would want to use Diamond or MMseqs2 instead of BLAST+?

Thomieh73 commented 2 years ago

Just a comment on GenericRepeatFinder, it has a bioconda package: https://anaconda.org/bioconda/genericrepeatfinder you can add that to the Readthedocs installation instructions