Comments (5)
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
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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.
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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
from genomad.
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
from genomad.
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! :)
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Related Issues (20)
- Error with geNomad v1.8.0, missing tensorflow.keras HOT 5
- mmseqs2 error HOT 3
- Different protein number from genomad and pyrodigal-gv HOT 2
- Small (reference) data for testing HOT 9
- Error while classifying sequences HOT 6
- Error mmseqs prefilter HOT 4
- genomad annotate fastq file is empty or contains multiple entries HOT 3
- plasmid classified as virus? HOT 7
- Optimization Request for Analyzing Large Number of MAGs with geNomad HOT 5
- Fewer viral contigs identified from genomad vs virsorter2 HOT 4
- The question about --disable-nn-classification HOT 1
- Provirus detection in genomad vs checkv HOT 6
- Error mmseqs prefilter HOT 2
- Genetic codes HOT 2
- question about integrase identification during provirus identification HOT 3
- How to export the viral DNA gene sequence? HOT 5
- Number of contigs in the assembly HOT 1
- Chromosome classification result HOT 2
- Discrepancy in Output Counts in Genomad HOT 1
- line 19 in aggregated_classfication.py HOT 2
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