1. Installing Snakemake
If you have properly installed Python 3.3+, just
> easy_install3 snakemake
or
> pip3 install snakemake
In case you have to install Python 3 yourself, we recommend to use the Miniconda Python 3 distribution is recommended.
With Miniconda installed, you can issue
> conda install -c bioconda snakemake

2. Running MTS
Make a directory for output, place config.yaml there, and configure it. Then run
> snakemake --directory <output directory>  --cores XX

3. Gathering stats
To render some interesting info, you need to specify some references in config:
REFS: path
or
REFS: [path1, path2, ...]
where path can be either a single reference or a folder with references.
Then run the stats target manually:
> snakemake --directory <output directory> stats_all
