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
Installing with pip¶
If you do not have conda, you can also install through pip:
python3 -m pip install poppunk
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)
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.