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Installation

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

conda install poppunk

Then run with poppunk.

Important

PopPUNK requires python3 to run (which on many default Linux installations is run using python3 rather than python).

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

Installing with pip

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

python3 -m pip install poppunk

You will also need mash (v2 or higher) installed (see :ref:`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 :ref:`scripts`.

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

Dependencies

We tested PopPUNK with the following packages:

  • python3 (3.6.3)
  • DendroPy (4.3.0)
  • hdbscan (0.8.13)
  • matplotlib (2.1.2)
  • networkx (2.1)
  • numpy (1.14.1)
  • numba (0.36.2)
  • pandas (0.22.0)
  • scikit-learn (0.19.1)
  • scipy (1.0.0)
  • sharedmem (0.3.5)

numba may need gcc >=v4.8 to install correctly through pip (if you are getting OSError or 'GLIBCXX_3.4.17' not found).

You will need a mash installation which is v2.0 or higher

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

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