Installation

INSTALLATION

MToolBox is compatible with Linux distributions and MacOS

Add the MToolBox path to your system PATH with the following command:

export PATH="/path/to/MToolBox/:$PATH"

then, from the MToolBox folder, run the install.sh script (for Linux distrib.):

./install.sh

to get a FULL installation of all the MToolBox dependencies. This may take a while, so please be patient until the full process is successfully completed. We STRONGLY recommend to use the default versions provided by the install script:

• GSNAP 2015-12-31.v7
• Anaconda distribution 2-2.5.0
• Zlib version 1.2.8
• MUSCLE version 3.8.31
• samtools version 1.3

The default Kmer value for GSNAP database generation is 15. However, if you want to change any of the previous versions or parameters when you run the full installation, please specify the following options:

./install.sh -g <gsnap_version> -a <anaconda_version> -z <zlib_version> -m <muscle_file> -s <samtools_version> -k <kmer_to_build_gsnap_db>

To re-install/update just one of the MToolBox software dependencies, please do:

./install.sh -i <software_name> 

where the possible software names are:

gsnap
anaconda
muscle
zlib
samtools
gsnap_db

For example, to update the GSNAP version, use:

./install.sh -i gsnap -g 2016-05-25

To get the install help:

./install.sh -h

As of 24 October 2017, MToolBox can be also installed on MacOS by running:

./install.sh -o

for a FULL installation. All other options can be used as previously described, e.g.

./install.sh -o -g <gsnap_version>

to change the GSNAP version when installing the full pipeline on MacOS.