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Documentation for optional dependencies #201

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afrubin opened this issue Sep 15, 2021 · 1 comment · Fixed by #207
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Documentation for optional dependencies #201

afrubin opened this issue Sep 15, 2021 · 1 comment · Fixed by #207
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@alexismhill3

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@afrubin
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afrubin commented Sep 15, 2021

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+?
@afrubin afrubin mentioned this issue Sep 15, 2021
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@alexismhill3 alexismhill3 self-assigned this Sep 15, 2021
@Thomieh73
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Just a comment on GenericRepeatFinder, it has a bioconda package: https://anaconda.org/bioconda/genericrepeatfinder
you can add that to the Readthedocs installation instructions

@alexismhill3 alexismhill3 mentioned this issue Sep 30, 2021
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Make Opfi available on Bioconda alexismhill3/Opfi
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@Thomieh73 @afrubin @alexismhill3