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widdowquinn / pyani

Application and Python module for average nucleotide identity analyses of microbes.
http://widdowquinn.github.io/pyani/
MIT License
183 stars 54 forks source link

Pyani not installing through conda #419

Closed conmeehan closed 3 months ago

conmeehan commented 8 months ago

Summary:

When using conda to install the package, everything says it installs correctly but the pyani executable just isn't there.

Description:

Installation instructions followed as per github (environment then install) but used mamba instead. When I type 'pyani' on the command line, it just says command not found.

I also tried with pip3 and it didn't work for some reason.

Reproducible Steps:

mamba create --name pyani_env python=3.8 -y mamba activate pyani_env mamba install pyani pyani

Current Output:

N/A

Python Version:

3.8 inside the conda environment

Operating System:

OSX and Ubuntu (tried separately)

widdowquinn commented 8 months ago

Thanks for the report, Conor - this is an outstanding issue re: the landing page documentation. Many apologies that it's (still) not yet fixed and/or clear.

conda installs pyani v0.2; the pyani <command> syntax is new to pyani v0.3/development. For the conda-installed version, you'll need to follow this documentation: https://github.com/widdowquinn/pyani/blob/master/README_v_0_2_x.md

I hope that helps get things moving.

Cheers,

L.

conmeehan commented 8 months ago

Hi,

Yes that clears it up a bit. That means that to use pyani the conda doesn't work at all? I have to install from source?

C

widdowquinn commented 8 months ago

Sadly, yes. The average_nucleotide_identity.py script runs with the conda installation, but the pyani <XXXX> form does not.

conmeehan commented 8 months ago

Ok no worries, I can work with that. Thanks!

C

widdowquinn commented 3 months ago

Only closing because it's an idle issue - please do reopen if you need to.