Conda environment not named

Question

[Begonia_pavonina]

I have installed snakemake with conda as following:

conda create --yes -c conda-forge -c bioconda -n snakemake snakemake   

But the environment has not the name "snakemake" I have put in the above command. There is only the full path indicated.

 conda info --envs                                     
# conda environments:                                                         
# base                  *  /mnt/shared/home/usr/mambaforge     
    mamba                  /mnt/shared/home/usr/mambaforge/envs/mamba                    
                           /mnt/shared/scratch/usr/apps/conda                            
                           /mnt/shared/scratch/usr/apps/conda/envs/snakemake

And I have to call it using the full path to call the snakemake environment.

Would anyone know why the environment is not named?

Answer 1

[Nitin Narwade]

There are two different conda installations on your system. When you are activating an environment from one conda (/shared/home/usr/mambaforge) the other (/mnt/shared/scratch/usr/apps/conda) is not loading properly, as it may have misconfigured with the same configuration file in /home/user/.conda. This could be one of the possible explanations.

I think you can still activate these environments using a complete path.

Regards,
Nitin N.

[Begonia_pavonina]

Thank you Nitin. I though that /mnt/shared/home/usr/mambaforge was just in my base environment, and /mnt/shared/scratch/usr/apps/conda just accessible in the mamba environment.

In this case, do you think the best fix would be to erase the /mnt/shared/scratch/usr/apps/conda file?

[Nitin Narwade]

Yes, I would prefer keeping only one conda installation on a system.

Regards,

Nitin N.