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
To assemble a dataset, you need to prepare a config.yaml. Use the provided template, it's mostly self-descriptive. Then run
> ./mts.py -c <config> -t XX --directory <output directory>

3. Gathering stats
To enable stats for some stage(s), add the section to the config:
stats:
    stage: [stat1, stat2]
"gf" stats require references provided with "refs" parameter:
    refs: path
or
    refs: [path1, path2, ...]
where path can be either a single reference or a folder with references.
