Run MToolBox¶
MToolBox is made by several snakemake workflows which can be run independently. We provide wrappers for the most common tasks and analyses. Using these wrappers will save a lot of typing and headache for the lazy users (probably you). Cool, isn’t it? :)
All the wrappers accepts snakemake arguments and parse automatically the config.yaml configuration file required by snakemake.
Setting up a working directory¶
Replace /path/to/MToolBox/dir/ with the MToolBox installation path and /path/to/analysis/dir with the folder where you wish to run your analysis.
export MTOOLBOX_DIR=/path/to/MToolBox/dir/
cd /path/to/analysis/dir
cp $MTOOLBOX_DIR/config.yaml .
cp $MTOOLBOX_DIR/cluster.yaml .
# create folders needed by the workflow
mkdir -p data/reads
mkdir -p data/genomes
mkdir -p logs/cluster_jobs
Copy read datasets to data/reads and genome fasta files to data/genomes.
# some code
How to run the MToolBox wrappers¶
Running the wrappers is as simple as this:
export PATH=/path/to/MToolBox/dir/:$PATH
MToolBox-<wrapper> <snakemake arguments>
E.g. if you want to run the MToolBox-variant-calling wrapper and print the commands it will execute, you can run
export PATH=/path/to/MToolBox/dir/:$PATH
MToolBox-variant-calling-bash -p
You can also display a graphical representation of the workflow by running
export PATH=/path/to/MToolBox/dir/:$PATH
MToolBox-variant-calling-bash --dag | display
This will show the workflow in a browser. Alternatively, you can save the workflow representation in a file by running
export PATH=/path/to/MToolBox/dir/:$PATH
MToolBox-variant-calling-bash --dag > workflow.svg