Installation

Install Anaconda

MToolBox_snakemake, an update of the MToolBox pipeline, is deployed in a conda environment, i.e. a virtual environment with all the needed tools/modules. Installing Anaconda is therefore essential, before installing the pipeline.

To this purpose, please follow instructions at http://docs.anaconda.com/anaconda/install/linux/ (hint: download the Anaconda installer in your personal directory with wget https://repo.continuum.io/archive/Anaconda3-2018.12-Linux-x86_64.sh).

Install MToolBox

MToolBox is hosted on GitHub. You can get a copy of the repository by running this commands:

cd /path/to/MToolBox_snakemake

# update git
conda install git

# fetch repo
git clone https://github.com/mitoNGS/MToolBox_snakemake.git

Installing MToolBox is as easy as running

cd MToolBox_snakemake
bash install.sh

The setup script install.sh will:

  • install the mtoolbox conda environment with all the required dependencies
  • create a command (mtoolbox-activate) which will be used to activate the MToolBox conda environment and add the folders of MToolBox executables and utilities to your PATH.