## Installation

> Note that to run mOTUs you would need a 64-bit Linux or MacOS system with at least 16 GB of RAM.
### Using conda

We suggest that you install mOTUs through [conda](https://anaconda.org/bioconda/motus) in order to automatically handle all the necessary dependencies. It is recommended to install the package in a new environment:
```bash
conda create -n motus-env
conda install -n motus-env -c bioconda motus
```

It can happen that the latest package version is not installed. This is usually because the correct dependencies were not installed. In this case you can try specifying the version you want while installing:

```bash
conda install -n motus-env -c bioconda motus>=3.0
```

If this still does not work, you can try installing using pip or github (see below).


### Using pip

You have to first install the dependencies on your own. Here is the list of dependencies:

1. Python 3.6.5 or higher [https://www.python.org/downloads/](https://www.python.org/downloads/)
2. samtools 1.6 or higher [https://github.com/samtools/samtools](https://github.com/samtools/samtools).
3. bwa 0.7.17 or higher [https://github.com/lh3/bwa](https://github.com/lh3/bwa).
4. metaSNV 1.0.3 [http://metasnv.embl.de/](http://metasnv.embl.de/) *optional as it is required only for command `snv_call`*


You can then install using [pip](https://pypi.org/project/motu-profiler/):

```bash
# Download and install mOTUs
python -m pip install motu-profiler
# Download the mOTUs database ~3.5 GB; this can take a few min
motus downloadDB
```


### Install from GitHub

You would need to install the dependencies on your own. See [above](#using-pip) for the list of dependencies.


```bash
git clone https://github.com/motu-tool/mOTUs.git #latest version
cd mOTUs
python setup.py install
motus downloadDB

#if you are unable to execute motus you might need to add the path of the executable to your .bashrc file
cd motus
echo export PATH=`pwd`:$PATH >> ∼/.bashrc
source ∼/.bashrc
```


### Check installation

In all cases you can test that mOTUs is installed correctly with:

```
motus profile --test
```



### QIIME2

mOTUs is also offered as a plugin for QIIME2. Further information can be found at [this link](https://library.qiime2.org/plugins/motus/45/).