use AGAT::AGAT

[antzellie]

Describe the bug I installed all the code and perl modules for AGAT, and I am trying to run agat_sp_add_introns.pl However, I keep on getting an error message (as seen in the screenshot attached). I have updated all my packages and perl, but I can't seem to fix this problem. Am I missing a step?

General (please complete the following information):

• AGAT version Version v0.8.0
• AGAT installation/use: Installed using Conda
• OS: Ubuntu 24.04

Screenshots

[Juke34]

Did you install AGAT via conda or only the dependencies? If you installed AGAT via conda did the installation went well? Did you activate / use the correct env?

[antzellie]

Hi.

I assume it was done correctly, these are some screenshots of what I did.

And yes, I did activate by using 'conda activate agat'

[Juke34]

Could you run
config --add channels bioconda conda config --add channels conda-forge conda config --set channel_priority strict

And then try again in a fresh env:
Conda create -n agat_fresh agat. Activate the new env:
conda activate agat_fresh

And try agat

[antzellie]

Thank you for the suggestion. I will try it and let you know if I still have any issues.

On Fri, 27 Sept 2024, 21:56 Jacques Dainat, @.***> wrote:

Could you run config --add channels bioconda conda config --add channels conda-forge conda config --set channel_priority strict

And then try again in a fresh env: Conda create -n agat_fresh agat. Activate the new env: conda activate agat_fresh

And try agat

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[antzellie]

Hello. So I tried running the "config --add channels bioconda" commmand but it says that the config command is not found. I did try and do it in roott with "sudo" but that still didn't work. I am doing this in Ubuntu.

[Juke34]

Right the correct command is conda config --add channels bioconda conda config --add channels conda-forge conda config --set channel_priority strict

[antzellie]

Hi. Thank you for all the assistance, I got it all sorted, it is running now.