Using Microbiome Modelling Toolbox with Gurobi?

[nickp60]

Is it possible to configure the Microbiome Modelling toolkit to use Gurobi? It appears that modern releases of CPLEX are unsupported, and I am not able to run generateMexFastFVA successfully, where I get the error:

generateMexFastFVA()
 > isCompatible: The compatibility can only be verified on the following mac OS versions: macOS 10.13+.
 > isCompatible: The solver compatibility cannot be verified with MATLAB R2024b.
Warning: As the ibm_cplex interface is not compatible, the generated MEX file might
not be compatible. 
> In generateMexFastFVA (line 34) 
 > The exact version of CPLEX could not be determined
Error using generateMexFastFVA (line 80)
The directory /include/ilcplex does not exist. Please install the CPLEX solver as
explained here.
 

I set changeCobraSolver('gurobi','LP'); but mgPipe still falls back to CPLEX.

I'm running '24.2.0.2863752 (R2024b) Update 5' on MacOS 14.6.1.

[almut-heinken]

Dear Nick,
the MMT should still work with Gurobi. CPLEX is required for using fastFVA. If another solver is used instead, the fluxVariability function should instead used for the prediction of metabolic profiles (which takes longer). The model building pipeline should not be affected. Let me know if the pipeline goes through using fluxVariability.
Best regards,
Almut

[nickp60]

This is great, thanks! How do I enable fluxVariability? I see references in this module but I'm uncertain how to prevent it from using FastFVA (short of uninstalling CPLEX).

[almut-heinken]

Dear Nick,
if fastFVA cannot run because CPLEX is not functional, then it should be skipped automatically and the normal FVA should be used instead. Let me know if that is not the case.