.. highlight:: shell ============ Installation ============ CarveMe can be easily installed using the **pip** package manager: .. code-block:: console $ pip install carveme Additionally, you must manually install the diamond_ sequence aligner: .. code-block:: console $ 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). .. code-block:: console $ conda install --c conda-forge pyscipopt Also, remember to select the correct solver during execution: .. code-block:: console $ carve [ARGS] --solver scip .. _diamond: https://github.com/bbuchfink/diamond .. _SCIP: https://scipopt.org .. _CPLEX: https://www.ibm.com/analytics/cplex-optimizer .. _Gurobi: https://www.gurobi.com/downloads/gurobi-software .. _documentation: https://www.ibm.com/support/knowledgecenter/SSSA5P_12.7.1/ilog.odms.cplex.help/CPLEX/GettingStarted/topics/set_up/Python_setup.html Everything should be ready now! See the next section for instructions on how to start *carving*.