Installation

We suggest to install mOTUs through conda:

conda install -c bioconda motus

Otherwise you can install using pip:

# Download and install mOTUs
pip install motu-profiler
# Download the mOTUs database
motus downloadDB

where you have to install the depndecies on your own. For example you could create a conda enviroment:

conda env create -f env/mOTUs_v2.yaml
source activate mOTUs_v2

You can test that motus is intalled correctly with:

motus profile --test

Install from GitHub

Clone the motus repository:

git clone https://github.com/motu-tool/mOTUs_v2.git

Run setup.py:

python mOTUs_v2/setup.py 

There are four steps:

1. Download the ZIP motus database.
2. Extract the files into db_mOTU directory.
3. Remove the ZIP archive.
4. Create a file with the motus tool version information

It is recommended to add the git repository to the system path.

You can run test.py to check the motus installation and pre-requisites:

python mOTUs_v2/test.py 

The expected result is:

 ------------------------------------------------------------------------------
|                               TEST MOTUS TOOL                                |
 ------------------------------------------------------------------------------

1-- ran setup.py: done

2-- Tools and versions:
- python:    correct
- bwa:       correct
- samtools:  correct
- metaSNV:   correct

3-- Taxonomy profiling test:
- Run motus (-v 1, only error messages):
- end motus call

Check resulting profile: correct

Install dependencies with conda

If you have conda, you can install the dependencies and create an enviroment:

cd mOTUs_v2/env
conda env create -f mOTUs_v2.yaml
source activate mOTUs_v2