Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Older versions of mafft and tools depending on it are not installable if conda-forge is higher than bioconda #50086

Open
warownia1 opened this issue Aug 15, 2024 · 2 comments

Comments

@warownia1
Copy link
Contributor

Following the setup instruction on the bioconda website I configured the channels as following:

conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

which puts the channels in the following order

channels:
  - conda-forge
  - bioconda
  - defaults

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.

@aliciaaevans
Copy link
Contributor

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

@warownia1
Copy link
Contributor Author

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants