Installation

Install Anaconda (or Miniconda) and mamba

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 (or Miniconda) is therefore essential, before installing the pipeline. You may want to install Miniconda to keep your installation smaller (since Anaconda comes with ~1500 prebuilt packages which you may not need!).

Please find instructions to install Anaconda here and Miniconda here.

Please note: MToolBox_snakemake has not been tested on Windows. In order to use MToolBox_snakemake on Windows, we strongly recommend to use the Docker container <link>.

Once Anaconda or Miniconda are installed, we also strongly recommend to install mamba to install the MToolBox_snakemake conda environment:

conda install -c conda-forge mamba

Install MToolBox-snakemake

We recommend to download MToolBox-snakemake by cloning the official repo on GitHub:

# Pick a folder for your installation
# and replace /path/to/MToolBox_snakemake with it
cd /path/to/MToolBox_snakemake

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

Please note: you could also conveniently download MToolBox-snakemake at this link, but by doing so you will miss the chance to easily integrate future updates!

Once you have cloned (or downloaded and unzipped) the repo, installing MToolBox should be 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.

Note

The install.sh will create the alias mtoolbox-activate in the ~/.bash_profile file, so be sure it get sourced!