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. Installing pre-requisites
MTS requires some Python packages which may be installed via Conda:
> conda install biopython
> conda install pandas
Additional software that requires Python 2.x (CONCOCT, CheckM etc.) must be installed in a dedicated conda environment:
> conda create -n mts27 python=2.7
> conda activate mts27
> <software-specific installation>

3. Building MTS
MTS binaries are built as a SPAdes subproject:
> cd assembler
> make -C build/release/project/mts

4. Running MTS
To assemble a dataset, you need to prepare a config.yaml. Use the provided template, it's mostly descriptive. Then run
> ./mts.py -c <config> -t XX <output directory>
You may also put config.yaml in the output directory and omit the -c parameter.
For all arguments, run ./mts.py -h

5. Examining results
Resulting bins are placed in binning/bins output subdirectory, reassembled ones in reassembly/bins. Stats (if enabled) are placed in stats/summary.
