Cannot install pangolin with conda v4.12.0

[josesho]

Hello,

Using conda v4.12.0, I run the command

conda create -n pangolin-py3.9 -c bioconda -c conda-forge -c defaults python=3.9 pangolin

which quickly runs into the following error:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: \ 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                                            

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

Output in format: Requested package -> Available versions

Package python conflicts for:
pangolin -> constellations[version='>=0.0.15'] -> python[version='>=3|>=3.10,<3.11.0a0|>=3.10,<3.11.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.9,<3.10.0a0|>=3.5',build=*_cpython]
python=3.9
pangolin -> python[version='>=3.6|>=3.7']

Which seems to me that the required python version for constellations has a conflict with the one required for pangolin?? Even though it seems there shouldn't be? Not sure if I am missing anything.

Any help is appreciated, thanks!

EDIT: I tried the development route with

git clone https://github.com/cov-lineages/pangolin.git
cd pangolin
conda env create -f environment.yml

and it also failed, but for seemingly different reasons.

Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound: 
  - gofasta
  - pip=19.3.1
  - usher[version='>=0.5.4']
  - minimap2[version='>=2.16']
  - ucsc-fatovcf[version='>=426']

[aineniamh]

Hi @josesho, I'm not sure what's causing your issue. The error suggests that it's a python version issue, although both versions should be compatible with 3.9.

If you try with

conda create -n pangolin-env -c bioconda -c conda-forge -c defaults  pangolin

Does that solve the environment?

[synmuh]

Hello, seems there is some issue installing pangolin v4.1.1. Using miniconda environment and Ubuntu 22.04 LTS

[aineniamh]

Try running the command described here: #471 (comment)

conda create -n pangolin -c bioconda -c conda-forge  pangolin=4.1.1
conda activate pangolin

pangolin --help

[josesho]

Hi @aineniamh ,

Still no dice...

Running the following

conda create -n pangolin -c bioconda -c conda-forge -c defaults pangolin

on an M1 Max MacBook Pro produces

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

UnsatisfiableError: 

while running

conda create -n pangolin -c bioconda -c conda-forge -c defaults pangolin=4.1.1

produces a slight variation...

Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: \ 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

PackagesNotFoundError: The following packages are not available from current channels:

  - gofasta

Current channels:

  - https://conda.anaconda.org/bioconda/osx-arm64
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-arm64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

Not sure how else to proceed?

[josesho]

OK, I was able to successfully install on an x86 cluster using

conda create -n pangolin -c bioconda -c conda-forge -c defaults pangolin=4.1.1

So that solves the issue partially.

Seems like ARM-based systems like the M1 / M2 will take some time before this is ironed out?

[lab01atgc]

If you follow these steps from the Nextstrain installation site it will work
Step 1 - create a special conda env
Step 2 - while you are in the special conda env create the new pango conda env running

conda create -n pangolin -c bioconda -c conda-forge -c defaults pangolin=4.1.1

tested on m1 Mac and works !

Source: ( look at native install tab ) https://docs.nextstrain.org/en/latest/install.html

If using a newer Mac with an Apple silicon chip (e.g. M1), first run these commands to ensure Conda creates the environment with osx-64 emulation:

Create a new environment using Intel packages called base_osx-64

CONDA_SUBDIR=osx-64 conda create -n base_osx-64 python

Activate new Intel-based environment

conda activate base_osx-64

Ensure future Conda commands in this environment use Intel packages too.

conda config --env --set subdir osx-64