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-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
mtoolboxconda 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 yourPATH.