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Trying to install t-coffee I noticed that it cannot be installed due to the conflict with mafft library. It requires mafft=7.310 which is not installable.
After some investigation I found that having conda-forge channel on top makes it impossible to install versions of mafft from bioconda either explicitly or implicitly.
The command mamba install --dry-run mafft=7.310 fails with
Could not solve for environment specs
The following package could not be installed
└─ mafft 7.310** is not installable because it conflicts with any installable versions previously reported.
This error is not specific to version 7.310. All versions except for conda-forge::mafft cannot be installed.
Why has mafft been moved to conda-forge and is no longer present in the bioconda-recipes repository? It causes environment resolving issues now.
The text was updated successfully, but these errors were encountered:
Can you try mamba install -c bioconda mafft=7.310 in a fresh environment? If that doesn't work, what OS and arch are you using? I am able to install that version and also t-coffee on Linux x86_64.
For the reason someone decided to add it to conda-forge, here's the original PR which has some discussion: conda-forge/staged-recipes#25606
It does work when I put bioconda on top of the channels list either with conda config or -c bioconda but that means I have to change channels order for installing different packages and their dependencies. It is not possible when creating envs from the exported environemnt.yaml files.
Following the setup instruction on the bioconda website I configured the channels as following:
which puts the channels in the following order
Trying to install t-coffee I noticed that it cannot be installed due to the conflict with mafft library. It requires mafft=7.310 which is not installable.
After some investigation I found that having conda-forge channel on top makes it impossible to install versions of mafft from bioconda either explicitly or implicitly.
The command
mamba install --dry-run mafft=7.310
fails withThis error is not specific to version 7.310. All versions except for
conda-forge::mafft
cannot be installed.Why has mafft been moved to conda-forge and is no longer present in the bioconda-recipes repository? It causes environment resolving issues now.
The text was updated successfully, but these errors were encountered: