Conda install Figtree

Question

Using Anaconda on Linux I tried this:

 conda install -c bioconda figtree 

But it gives me this:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: | 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abor/ 
failed                                                                                                                                        

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Maybe it's just me but isn't this an unhelpful message? What does Output in format: Requested package -> Available versionsmean? Are they just trying to be mean?

Shouldn't I be searching for answers elsewhere? It does not seam right to ask here

And most importantly: how do I solve this and similar issues in the future? With or without Anaconda

Answer 1

The Bioconda has channel configuration settings that users need to follow in order to get the expected behavior from Bioconda packages including solving for installs. In particular, users should have conda-forge > bioconda > defaults. This could be what is affecting the installation, since figtree has xorg-libxtst as a dependency and that is only on Conda Forge.

If you want to do this ad hoc (as in OP), the command that would mimic their recommended settings would be

conda install --override-channels -c conda-forge -c bioconda -c defaults figtree 

where the order of channels defines their precedence.

However, it is usually better practice to configure this either globally (what the Bioconda docs show) or on a per-environment basis (for users with a diversity of projects):

# activate environment
conda activate my_env

# set channels for environment
conda config --env --add channels defaults
conda config --env --add channels bioconda
conda config --env --add channels conda-forge

# no need to use ad hoc `-c` flags
conda install figtree