Problems with installation

[agg437]

Hello everybody,

I was trying to install ete3 in a conda environment of Linux with the following lines of code:
conda create -n ete3 python=3
conda activate ete3
conda install -c etetoolkit ete3 ete_toolchain

I am having problems with the last one, the error I got:

LinkError: pre-link script failed for package etetoolkit::ete3-3.0.0b35-py_0
location of failed script: /home/ana/miniconda3/pkgs/ete3-3.0.0b35-py_0/bin/.ete3-pre-link.sh
==> script messages <==

==> script output <==
stdout:
stderr: + /home/ana/miniconda3/envs/ete3/bin/python /home/ana/miniconda3/pkgs/ete3-3.0.0b35-py_0/link.py
/home/ana/miniconda3/pkgs/ete3-3.0.0b35-py_0/bin/.ete3-pre-link.sh: line 2: /home/ana/miniconda3/envs/ete3/bin/python: No such file or directory
return code: 127

I also tried to install it with the last version of python available but I did not succeed.
Thank you in advance for the help,
Best regards,
Ana González Guerra

[jhcepas]

Hi Ana,
this seems a problem with your conda environment (even the python binary is not executing?).
Could you try a clean conda installation? Then, unless you are planning to use the ete build command line, you can skip the installation of ete_toolchain and just install ete3.

[agg437]

Hi Jaime, I tried with that but later I had problems with the import part

[marco-mariotti]

Hi Ana, Jaime, I had this problem myself when I installed ete3 from scratch a few weeks ago. If I remember correctly, I had the impression that the initial python installed upon environment creation was a higher version than the one ete3 accepted, so that when conda was installing ete3, it was trying to downgrade it, and that's the bit in the ete3 installation that crashed for some reason. Anyhow, in my case the problem was fixed when I installed the latest version of ete3. In fact, no idea why, but in my computer and it seems in yours too, conda is not correctly selecting the latest version (Jaime, any idea why?). Anyhow, bottom line, try this as your last command, see if it works: conda install -c etetoolkit ete3==3.1.2 ete_toolchain ciao,

…

On Wed, Jun 30, 2021 at 9:12 PM Jaime Huerta-Cepas ***@***.***> wrote: Hi Ana, this seems a problem with your conda environment (even the python binary is not executing?). Could you try a clean conda installation? Then, unless you are planning to use the ete build command line, you can skip the installation of ete_toolchain and just install ete3. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#554 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACTXRIHIUYDONCTNOWFUQJDTVNUBTANCNFSM47SB7OMA> .

-- Marco Mariotti Ramón y Cajal Fellow, Group Leader Department of Genetics, Microbiology and Statistics Universitat de Barcelona https://www.mariottigenomicslab.com/

[jhcepas]

there is actually a number of issues that might be related to this (e.g., #542 #543) happening since 3.1.2 (and perhaps changes in conda defaults and python versions). Didn't have time to debug it myself yet (if anyone solves it, please send a PR)
As a temporary solution, you could always install basic dependencies with conda (qt, pyqt, six, numpy) and ETE with pip from the master branch:
pip install https://github.com/etetoolkit/ete/archive/refs/heads/master.zip

[jhcepas]

brief update: installing without ete_toolchain seems to work just fine. ete_toolchain is only required by the ete build command and will be replaced by bioconda dependencies anyways. working on it...

conda install -c etetoolkit ete3 

[agg437]

Hi Marco,Jaime,
The command conda install -c etetoolkit ete3==3.1.2 ete_toolchain seems to work except for the package slr, I guess that if this package is not totally necessary, I can go on with this installation until ete dependencies are available from bioconda.
Thank you so much both for the help and support, I will continue practising with the tool (it seems very useful and smart).