Installation

The easiest way to install is through conda, which will also install the dependencies:

conda install poppunk

Then run with poppunk.

Important

From v2.1.0 onwards, PopPUNK requires python3.8 to run (which on many default Linux installations is run using python3 rather than python).

Important

From v2.1.2 onwards, PopPUNK no longer supports mash. If you want to use older databases created with mash, please downgrade to <v2

Installing with conda (recommended)

If you do not have conda you can install it through miniconda and then add the necessary channels:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Then run:

conda install poppunk

If you are having conflict issues with conda, our advice would be:

• Remove and reinstall miniconda.
• Never install anything in the base environment
• Create a new environment for PopPUNK with conda create -n pp_env poppunk

If you have an older version of PopPUNK, you can upgrade using this method – you may also wish to specify the version, for example conda install poppunk==2.3.0 if you wish to upgrade.

conda-forge also has some helpful tips: https://conda-forge.org/docs/user/tipsandtricks.html

Installing with pip

If you do not have conda, you can also install through pip:

python3 -m pip install poppunk

This may not deal with all necessary Dependencies.

Clone the code

You can also clone the github to run the latest version, which is executed by:

git clone https://github.com/johnlees/PopPUNK.git && cd PopPUNK
python3 poppunk-runner.py

This will also give access to the Scripts.

You will need to install the Dependencies yourself (you can still use conda or pip for this purpose).

Dependencies

We tested PopPUNK with the following packages:

• python3 (3.8.2)
• pp-sketchlib (1.5.1)
• DendroPy (4.3.0)
• hdbscan (0.8.13)
• matplotlib (2.1.2)
• graph-tool (2.31)
• numpy (1.14.1)
• pandas (0.22.0)
• scikit-learn (0.19.1)
• scipy (1.0.0)
• sharedmem (0.3.5)

Optionally, you can use rapidnj if producing output with --microreact and --rapidnj options. We used v2.3.2.