aragorn package does not exist

[sophiaaredas]

Hello! I am trying to install geNomad using mamba. However, it will not install because it says that aragorn does not exist error: the following package could not be installed. aragorn does not exist (perhaps a typo or a missing channel)

It is not an issue with my typing and from what I have seen it appears that my channels are fine. That being said I am new to bioinformatics and would appreciate any help. I would love be able to start using geNomad:)

[apcamargo]

Hi @sophiaaredas

Aragorn is in Bioconda, so you shouldn't have any problems installing it from there. Are you sure you included Bioconda in the command?

mamba create -n genomad -c conda-forge -c bioconda genomad

[sklucas]

Hi @apcamargo, I am having this issue as well. MacOS Ventura 3.5.1. Fresh miniforge install. Result from the mamba install code is:

pkgs/main/osx-arm64                                           No change
pkgs/r/noarch                                                 No change
bioconda/osx-arm64                                            No change
pkgs/main/noarch                                              No change
pkgs/r/osx-arm64                                              No change
bioconda/noarch                                    @   2.3MB/s  2.2s
conda-forge/osx-arm64                              @   3.5MB/s  2.3s
conda-forge/noarch                                 @   5.2MB/s  2.9s
Could not solve for environment specs
The following package could not be installed
└─ genomad   is uninstallable because it requires
   └─ aragorn  , which does not exist (perhaps a missing channel).

At least for me this seems like a Mac-specific issue as I just installed geNomad on a CentOS Linux server using mamba yesterday and it went smoothly. I will use the Docker image for now, but thought I would add that this happened to me too.

[apcamargo]

Hi @sklucas That's strange. I installed geNomad on a Mac before. Did you copy and paste the exact command below? Are you using a M1/M2 Mac?

mamba create -n genomad -c conda-forge -c bioconda genomad

[sklucas]

Hi @apcamargo the issue is on an M2 Mac. I just installed geNomad successfully using the code above with the latest Miniforge on an Intel Mac and it was successful. I will have to do some digging around to figure out what is happening with the new setup. Seems like the issue is bigger than the scope of this one package. You have provided many other ways to install/use the geNomad though, which is much appreciated!

Edit: This install method works:

mamba create -n genomad
mamba activate
conda config --env --set subdir osx-64     
mamba install -c conda-forge -c bioconda genomad    

[apcamargo]

So it does seem to be a problem with the architecture. I guess we will have to wait until they start building for ARM.

Good to know that you managed to install it! :)