Lesson 4: Channel Priority and Best Practices

How Conda resolves packages

When you install a package, Conda searches channels in order. The first channel that provides a compatible package is used. This is why channel priority matters.

If the channel order is not consistent, you can get incompatible builds or dependency conflicts.

Best practice for bioinformatics

A common and reliable channel order is:

1. conda-forge
2. bioconda

This ensures that bioconda packages use dependencies from conda-forge.

Note: Many bioinformatics workflows avoid the defaults channel to reduce licensing risk and dependency conflicts.

Remove the defaults channel

This command removes defaults from your channel list.

conda config --remove channels defaults

Add conda-forge

This command adds conda-forge at the top of your channel list.

conda config --add channels conda-forge

Add bioconda

This command adds bioconda below conda-forge.

conda config --add channels bioconda

Enable strict channel priority

This command forces Conda to use the highest-priority channel possible for each package.

conda config --set channel_priority strict

Verify channel order

This command shows your configured channels. The expected order should place conda-forge before bioconda.

conda config --show channels

Expected output order:

channels:
  - conda-forge
  - bioconda

If you find that bioconda is above conda-forge, you can run the following command to fix the order:

conda config --add channels conda-forge

This will move conda-forge to the top of the list, ensuring that it has higher priority than bioconda.