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 in order to automatically handle all the necessary dependencies. It is recommended to install the package in a new environment:
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:
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:
Python 3.6.5 or higher https://www.python.org/downloads/
samtools 1.6 or higher https://github.com/samtools/samtools.
bwa 0.7.17 or higher https://github.com/lh3/bwa.
metaSNV 1.0.3 http://metasnv.embl.de/ optional as it is required only for command
snv_call
You can then install using pip:
# 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 for the list of dependencies.
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