Bioconda channel order - Githubissues

lenorakepler commented 2 years ago

This may be something specific to my configuration, but wanted to point out in case it helps anyone else.

I was having an issue installing a standalone staramr environment (for 0.9.1 or 0.7.2) with the command as suggested: mamba create -c bioconda -c conda-forge -c defaults --name staramr staramr==0.7.2 pandas==1.1.5 mlst==2.19.0

This would result in the mamba error: Encountered problems while solving:

package staramr-0.7.2-py_0 requires biopython >=1.70, but none of the providers can be installed

I read elsewhere that bioconda is strict about channel order, and if things are not installed in the order conda-forge > bioconda > defaults, it can cause issues, so I changed around the 'mamba create' command to:

mamba create -c conda-forge -c bioconda -c defaults --name staramr staramr==0.7.2 pandas==1.1.5 mlst==2.19.0

and was able to successfully create the environment.

Thanks for a fabulous tool! Lenora

apetkau commented 2 years ago

Thanks so much for pointing this out @lenorakepler . This will be fixed in https://github.com/phac-nml/staramr/pull/163

apetkau commented 1 year ago

Fixed in https://github.com/phac-nml/staramr/pull/163

phac-nml / staramr

Bioconda channel order #162