CarveMe currently supports Python 3.6 and 3.7. We recommend using the Anaconda python distribution.

CarveMe can be easily installed using the pip package manager:

$ pip install carveme

Additionally, you must manually install two external dependencies:

  • diamond (conda install -c bioconda diamond)
  • IBM CPLEX Optimizer

Note that you will need to register with IBM to obtain an academic license for CPLEX.

IMPORTANT: After installing CPLEX, do not forget to install the CPLEX python API (see the CPLEX documentation for details).

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