Installation

CarveMe can be easily installed using the pip package manager:

$ pip install carveme

Additionally, you must manually install the diamond sequence aligner:

$ conda install -c bioconda diamond

Solver

You also need an optimization solver. The recommended option is to install either IBM CPLEX or Gurobi. You need a full version with the respective academic license (demo version will not work).

After installing CPLEX, do not forget to install the CPLEX python API.

Alternatively, you can use the open source SCIP solver. This will be slower (expect at least 10 min per execution).

$ conda install --c conda-forge pyscipopt

Also, remember to select the correct solver during execution:

$ carve [ARGS] --solver scip

Everything should be ready now! See the next section for instructions on how to start carving.