Running MToolBox

###RUNNING MTOOLBOX

Add MToolBox to your system PATH with the following command:

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

Then, in the directory where you want to execute MToolBox, run the pipeline as following:

MToolBox.sh -i <conf.sh>

Please note that you MUST specify the -i option that takes a config file as an argument, inside of which the user MUST specify 2 mandatory arguments:

input_type=
ref=

where input_type can accept bam|fastq|fastq.gz|fasta|sam, and ref can accept RSRS|RCRS. An example of the config file required by MToolBox is provided by the test_rCRS_config.sh file. All the other arguments are OPTIONAL, if the default installation of MToolBox was successfully completed. In case the user would like to use some custom installation of the MToolBox software dependencies, please provide the FULL PATH to the installation as argument value. For further help, please read carefully the instructions within the test_rCRS_config.sh file here.

The MToolBox command must be executed inside the folder containing input files (where also output files will be placed) and config file, otherwise set the input_path and output_name value in the config file, if you want to specify different directories.

For a complete list of MToolBox.sh options please run as follows:

MToolBox.sh -h

Please note that only one of the supported input types at the time can be used within a single MToolBox run. MToolBox also accepts compressed fastq files (FASTQ.GZ).

IMPORTANT: if you want to run again MToolBox in the same folder, it is preferable that you delete all the files produced during the previous execution.