Pangolin installation with conda v24.1.2 is failing

[satya-lalam]

As suggested in the Pangolin installation documentation, executed the following command with conda v24.1.2
conda install -c bioconda -c conda-forge -c defaults pangolin

Error Output:

Channels:
 - bioconda
 - conda-forge
 - defaults
Platform: win-64
Collecting package metadata (repodata.json): done
Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides iqtree 1.6.12.* needed by pangolin-1.1-py_0

Could not solve for environment specs
The following packages are incompatible
└─ pangolin is not installable because there are no viable options
   ├─ pangolin [1.1|1.1.5] would require
   │  └─ iqtree 1.6.12.* , which does not exist (perhaps a missing channel);
   ├─ pangolin [1.1.11|1.1.13|...|2.3.0] would require
   │  └─ iqtree <2 , which does not exist (perhaps a missing channel);
   └─ pangolin [2.3.0|2.3.2|...|4.3] would require
      └─ gofasta, which does not exist (perhaps a missing channel).

I assume the Pangolin required package versions for iqtree and gofasta are not available in bioconda channel.

[huzuner]

This happens because of channel priorities. The conda-forge should take precedence over bioconda:

mamba install -c conda-forge -c bioconda -c defaults pangolin

You can also use mamba, it's faster.

This should also be changed in the documentation in the webpage.

[wm75]

Yes, the channel order should get documented correctly.

You can also use mamba, it's faster.

Latest versions of conda are now using libmamba to solve environments so conda instead of mamba should be fine again.