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 `_ 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 want to use GPUs, take a look at :doc:`gpu`. 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, but we are working on it and it should again be possible in an upcoming release. Clone the code -------------- You can also clone the github to run the latest version, which is executed by:: git clone https://github.com/bacpop/PopPUNK.git && cd PopPUNK python3 setup.py build python3 setup.py install python3 poppunk-runner.py This will also give access to the :ref:`scripts`. You will need to install the dependencies yourself (you can still use conda or pip for this purpose). See ``environment.yml``:: mamba env create -f environment.yml conda activate pp_env