ete3 install error from conda etetoolkit channel :(

[Courtney Stairs]

Hi there,

Crosspost to the BioStars for ETE3:https://www.biostars.org/p/9508370/#9508370

I'm trying to install etetoolkit via conda on MacOS and keep getting the same error. Google has been of very little help unfortunately, although I did find reference to similar errors at the bottom of this thread: https://github.com/etetoolkit/ete/issues/500, but these solutions did not work. I've also removed and reinstalled miniconda.

I ran the following:

    conda create -n ete3 python=3
    conda activate ete3
    conda install -c etetoolkit ete3 ete_toolchain

Then I get the following error indicating it cannot find python (weird):

    LinkError: pre-link script failed for package etetoolkit::ete3-3.0.0b35-py_0
    location of failed script: /PATH/TO/miniconda3/pkgs/ete3-3.0.0b35-py_0/bin/.ete3-pre-link.sh

    ==> script messages <==
    <None>
    ==> script output <==
    stdout:
    stderr: + /PATH/TO/miniconda3/envs/ete3/bin/python /PATH/TO/miniconda3/pkgs/ete3-3.0.0b35-py_0/link.py

    /PATH/TO/miniconda3/pkgs/ete3-3.0.0b35-py_0/bin/.ete3-pre-link.sh: line 2: /PATH/TO/miniconda3/envs/ete3/bin/python: No such file or directory
    return code: 127

I've tried putting python in the bin, but that did not solve the problem.

Does anyone have any ideas on how to solve this? I've been using this tool for years with no problem, but it seems like something has gone awry with the latest versions. FWIW, I can install it from the conda-forge channel... so i think its somethign with the newer builds?

Thanks! Please let me know if I can provide more info.
    

[dengzi...@gmail.com]

Hi,

we noticed this weird error and we are not able to recreate this error everytime. The most effective solution we have at the moment is separate the conda install into two steps:

conda install -c etetoolkit ete3

conda install -c etetoolkit ete_toolchain

Please give a try and let us know, thanks!

Cheers

[Courtney Stairs]

Wow - yep that worked. Thanks a lot. Past Courtney really wished she tried this earlier... 
Super super thank you!!

Courtney