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widdowquinn / pyani

Application and Python module for average nucleotide identity analyses of microbes.
http://widdowquinn.github.io/pyani/
MIT License
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pyani: command not found #406

Closed Gahyeon-K closed 1 year ago

Gahyeon-K commented 1 year ago

Summary:

I installed 'latest (master)' pyani package following instructions (https://pyani.readthedocs.io/en/latest/installation.html) using conda, pip, and source (source code from v0.2.11/ https://github.com/widdowquinn/pyani/archive/refs/tags/v0.2.11.tar.gz). But, the output was 'pyani: command not found', but 'average_nucleotide_identity.py: pyani 0.2.11'. So, Are there any issues in the compatibility of conda or python with pyani? I tried python versions 3.7, 3.8, and 3.10. Conda version is 4.13.0 I'll really appreciate for your solutions. Thanks!

widdowquinn commented 1 year ago

Hi @Gahyeon-K

As noted in #165 there are two versions of pyani. The command for v0.2, which is installed through pip/conda, is average_nucleotide_identity.py; the command for v0.3 is pyani (and the CLI is quite different). You have installed v0.2 so should use the instructions appropriate to that version: https://github.com/widdowquinn/pyani/blob/version_0_2/README.md

If you want to use v0.3, then please follow the instructions at https://github.com/widdowquinn/pyani#installation instead.

Many thanks,

L.