Installation¶

This section provides instructions for installation and configuration of pyMLST.

Automatic Installation¶

You can install pyMLST and their dependancy using bioconda:

conda install -c conda-forge -c bioconda pymlst

Manual Installation¶

From pypi repository:
```
pip install pymlst
```

From github source:

virtualenv venv
source venv/bin/activate
make install
make build

Dependancy¶

PyMLST uses 3 external tools to run alignment:

Mafft (>=7.307)
```
sudo apt install mafft
```
Blat (v35). You need to compile source or obtain executable at: https://genome.ucsc.edu/FAQ/FAQblat.html
kma (>=1.3) You need to compile source from: https://bitbucket.org/genomicepidemiology/kma/src/master/

Configuration¶

Configure the executable locations (if they are not on the PATH) and log level :

pyMLST configure --help
Usage: pyMLST configure [OPTIONS]

Configure executables paths and log level.

Options:
-b, --blat FILE   Blat executable absolute path.
-k, --kma FILE    Kma executable absolute path.
-m, --mafft FILE  Mafft executable absolute path.
-l, --log [DEBUG|INFO|WARNING|ERROR]
                  Level of logging, default=INFO
-r, --reset       Reset the configuration.
--help            Show this message and exit.